Quran 9:5 Kill the disbelievers wherever you find them ?!

9:5 Kill the disbelievers wherever you find them.

This ayah has been misquoted . First, we shall provide the verse in its context: 

فَإِذَا انسَلَخَ الْأَشْهُرُ‌ الْحُرُ‌مُ فَاقْتُلُوا الْمُشْرِ‌كِينَ حَيْثُ وَجَدتُّمُوهُمْ وَخُذُوهُمْ وَاحْصُرُ‌وهُمْ وَاقْعُدُوا لَهُمْ كُلَّ مَرْ‌صَدٍ ۚ فَإِن تَابُوا وَأَقَامُوا الصَّلَاةَ وَآتَوُا الزَّكَاةَ فَخَلُّوا سَبِيلَهُمْ ۚ إِنَّ اللَّـهَ غَفُورٌ‌ رَّ‌حِيمٌ ﴿٥﴾ وَإِنْ أَحَدٌ مِّنَ الْمُشْرِ‌كِينَ اسْتَجَارَ‌كَ فَأَجِرْ‌هُ حَتَّىٰ يَسْمَعَ كَلَامَ اللَّـهِ ثُمَّ أَبْلِغْهُ مَأْمَنَهُ ۚ ذَٰلِكَ بِأَنَّهُمْ قَوْمٌ لَّا يَعْلَمُونَ ﴿٦﴾

9:5-6 But when the forbidden months are past, then fight and slay the Pagans wherever ye find them, an seize them, beleaguer them, and lie in wait for them in every stratagem (of war); but if they repent, and establish regular prayers and practise regular charity, then open the way for them: for Allah is Oft-forgiving, Most Merciful. If one amongst the Pagans ask thee for asylum, grant it to him, so that he may hear the word of Allah. and then escort him to where he can be secure. That is because they are men without knowledge.

Having presented the verse in context, we can analyze it properly. Dr. Maher Hathout gives an explanation on the historical context of the verse:

This verse was revealed towards the end of the revelation period and relates to a limited context. Hostilities were frozen for a three-month period during which the Arabs pledged not to wage war. Prophet Muhammad was inspired to use this period to encourage the combatants to join the Muslim ranks or, if they chose, to leave the area that was under Muslims rule; however, if they were to resume hostilities, then the Muslims would fight back until victorious. One is inspired to note that even in this context of war, the verse concludes by emphasizing the divine attributes of mercy and forgiveness. To minimize hostilities, the Qur'an ordered Muslims to grant asylum to anyone, even an enemy, who sought refuge. Asylum would be granted according to the customs of chivalry; the person would be told the message of the Qur'an but not coerced into accepting that message. Thereafter, he or she would be escorted to safety regardless of his or her religion. (9:6). (Hathout, Jihad vs. Terrorism; US Multimedia Vera International, 2002, pp.52-53, emphasis added)

Therefore, this verse once again refers to those pagans who would continue to fight after the period of peace. It clearly commands the Muslims to protect those who seek peace and are non-combatants. It is a specific verse with a specific ruling and can in no way be applied to general situations. The command of the verse was only to be applied in the event of a battle. As Abdullah Yusuf Ali writes:

The emphasis is on the first clause: it is only when the four months of grace are past, and the other party show no sign of desisting from their treacherous design by right conduct, that the state of war supervenes - between Faith and Unfaith. (Yusuf Ali, The Holy Qur’an, Text, Translation and Commentary, emphasis added)

If the pagans would not cease their hostilities towards the Muslims, then they were to be fought, especially since they were living in the land of an Islamic state. Dr. Zakir Naik writes concerning this verse:

This verse is quoted during a battle. ...We know that America was once at war with Vietnam. Suppose the President of America or the General of the American Army told the American soldiers during the war: "Wherever you find the Vietnamese, kill them". Today if I say that the American President said, "Wherever you find Vietnamese, kill them" without giving the context, I will make him sound like a butcher. But if I quote him in context, that he said it during a war, it will sound very logical, as he was trying to boost the morale of the American soldiers during the war. ...Similarly in Surah Taubah chapter 9 verse 5 the Qur'an says, "Kill the Mushriqs (pagans) where ever you find them", during a battle to boost the morale of the Muslim soldiers. What the Qur'an is telling Muslim soldiers is, don't be afraid during battle; wherever you find the enemies kill them. Surah Taubah chapter 9 verse 6 gives the answer to the allegation that Islam promotes violence, brutality and bloodshed. It says: "If one amongst the Pagans ask thee for asylum, grant it to him, so that he may hear the word of Allah; and then escort him to where he can be secure that is because they are men without knowledge." [Al-Qur'an 9:6]
The Qur'an not only says that a Mushriq seeking asylum during the battle should be granted refuge, but also that he should be escorted to a secure place. In the present international scenario, even a kind, peace-loving army General, during a battle, may let the enemy soldiers go free, if they want peace. But which army General will ever tell his soldiers, that if the enemy soldiers want peace during a battle, don't just let them go free, but also escort them to a place of security? This is exactly what Allah (swt) says in the Glorious Qur'an to promote peace in the world. (SOURCE, emphasis added)

Dr. Naik makes some very interesting observations about the verse. Indeed, it is truly amazing how Islam-haters will ignore God's infinite mercy in their attempt to malign Islam. God has always given human beings a way out of any suffering, and has only ordained fighting as a last resort. Muslim scholars have written much commentary on these Qur'anic verses explaining the historical context in such great detail so that there may be no misconceptions. We have quoted extensively from various commentators on these verses and there is no need to repeat the same material again. We will provide one more commentary before moving on. Professor Shahul Hameed writes on verse 9:5:

This is a verse taken from Surah At-Tawba. This chapter of the Qur’an was revealed in the context when the newly organized Muslim society in Madinah was engaged in defending themselves against the pagan aggressors. The major question dealt with here is, as to how the Muslims should treat those who break an existing treaty at will. The first clause in the verse refers to the time-honored Arab custom of a period of warning and waiting given to the offenders, after a clear violation. That is, they will be given four months’ time to repair the damage done or make peace. But if nothing happens after the expiry of these forbidden months, what should be done? This is what the present verse says. According to this verse, fighting must be resumed until one of the two things happens: Either the enemy should be vanquished by relentless fighting. That is what is meant by {then fight and slay the pagans wherever ye find them, and seize them, beleaguer them, and lie in wait for them in every stratagem [of war]}; or they should repent, establish prayers and pay zakah, etc. This is one of those verses of the Qur’an which are likely to be misunderstood, if quoted out of context. We must understand that this fighting was against a people who forced the Prophet and his companions to leave not only their own homes but all their property and even their hometown of Makkah to Madinah. Once the Muslims were organized into a community in those lawless times, the rules to be followed by the Muslims were clearly laid down, even in the matter of war. Since Islam is a comprehensive system, no human activity could be ignored. And given the nature of mankind, we cannot imagine a situation where fighting is completely ruled out either. As can be seen, the above injunctions on fighting is not on an individual level, but only in the case of a society that strives to flourish and thrive as a nation. But even here the norms are clear: fighting is only in self defence or for the establishment of justice; and always fighting is the last option. And no one is allowed to transgress the limits set by God. (SOURCE, emphasis added)

Ibn al-`Arabi, in his commentary on the Qur’an, writes:

“It is clear from this that the meaning of this verse is to kill the pagans who are waging war against you.” (Ahkam al-Qur’an: 2/456, emphasis added)

Shaykh Sami al-Majid also makes some very interesting points in his discussion on this verse:

If we look at the verses in Sûrah al-Tawbah immediately before and after the one under discussion, the context of the verse becomes clear. A few verses before the one we are discussing, Allah says: “There is a declaration of immunity from Allah and His Messenger to those of the pagans with whom you have contracted mutual alliances. Go then, for four months, to and fro throughout the land. But know that you cannot frustrate Allah that Allah will cover with shame those who reject Him.” [Sûrah al-Tawbah: 1-2]
In these verses we see that the pagans were granted a four month amnesty with an indication that when the four months were over, fighting would resume. However, a following verse exempts some of them from the resumption of hostilities. It reads:
“Except for those pagans with whom you have entered into a covenant and who then do not break their covenant at all nor aided anyone against you. So fulfill your engagements with them until the end of their term, for Allah loves the righteous.” [Sûrah al-Tawbah: 4]
So when Allah says: “But when the forbidden months are past, then fight the pagans wherever you find them, and seize them and beleaguer them and lie in wait for them in every stratagem (of war)” we must know that it is not general, since the verse above has qualified it to refer to the pagan Arabs who were actually at war with the Prophet (peace be upon him) and those who broke their covenants of peace. This is further emphasized a few verses later where Allah says:
“Will you not fight people who broke their covenants and plotted to expel the Messenger and attacked you first?” [Sûrah al-Tawbah: 13] (SOURCE)

Therefore, the context of the verse within the Surah makes it clear that this refers to those who are persistent in their hostilities and attacks against Muslims, and it is applied in battle only. We recommend that one reads Shaykh Sami Al-Majid's full article entitled There is no Compulsion in Religion.

Quran 2:191 And slay them wherever ye catch them.

And slay them wherever ye catch them.." (2:191)

A classic and popular example of what Muslim scholars call a ‘cut and paste’ approach. Everything becomes so much easier for the Anti-Islamists when they remove the context. The solution is to simply replace the verse in its context:

وَقَاتِلُوا فِي سَبِيلِ اللَّـهِ الَّذِينَ يُقَاتِلُونَكُمْ وَلَا تَعْتَدُوا ۚ إِنَّ اللَّـهَ لَا يُحِبُّ الْمُعْتَدِينَ ﴿١٩٠﴾وَاقْتُلُوهُمْ حَيْثُ ثَقِفْتُمُوهُمْ وَأَخْرِ‌جُوهُم مِّنْ حَيْثُ أَخْرَ‌جُوكُمْ ۚ وَالْفِتْنَةُ أَشَدُّ مِنَ الْقَتْلِ ۚ وَلَا تُقَاتِلُوهُمْ عِندَ الْمَسْجِدِ الْحَرَ‌امِ حَتَّىٰ يُقَاتِلُوكُمْ فِيهِ ۖ فَإِن قَاتَلُوكُمْ فَاقْتُلُوهُمْ ۗ كَذَٰلِكَ جَزَاءُ الْكَافِرِ‌ينَ ﴿١٩١﴾ فَإِنِ انتَهَوْا فَإِنَّ اللَّـهَ غَفُورٌ‌ رَّ‌حِيمٌ ﴿١٩٢﴾ وَقَاتِلُوهُمْ حَتَّىٰ لَا تَكُونَ فِتْنَةٌ وَيَكُونَ الدِّينُ لِلَّـهِ ۖ فَإِنِ انتَهَوْا فَلَا عُدْوَانَ إِلَّا عَلَى الظَّالِمِينَ ﴿١٩٣﴾ الشَّهْرُ‌ الْحَرَ‌امُ بِالشَّهْرِ‌ الْحَرَ‌امِ وَالْحُرُ‌مَاتُ قِصَاصٌ ۚ فَمَنِ اعْتَدَىٰ عَلَيْكُمْ فَاعْتَدُوا عَلَيْهِ بِمِثْلِ مَا اعْتَدَىٰ عَلَيْكُمْ ۚ وَاتَّقُوا اللَّـهَ وَاعْلَمُوا أَنَّ اللَّـهَ مَعَ الْمُتَّقِينَ ﴿١٩٤﴾

2:190-194 Fight in the cause of God those who fight you, but do not transgress limits; for God loves not transgressors. And kill them wherever ye catch them, and turn them out from where they have turned you out; for persecution and oppression are worse than slaughter; but fight them not at the Sacred Mosque, unless they (first) fight you there; but if they fight you, kill them. Such is the reward of those who reject faith. But if they cease, God is Oft-Forgiving, Most Merciful. And fight them on until there is no more tumult or oppression, and there prevail justice and faith in God; but if they cease, let there be no hostility except to those who practice oppression. The prohibited month, for the prohibited month, and so for all things prohibited, there is the law of equality. If then any one transgresses the prohibition against you, transgress ye likewise against him. But fear (the punishment of) God, and know that God is with those who restrain themselves.

How many times do we see the above verse repeating the message to make it clear? These verse were revealed at a time when Muslims of Madinah were under constant attack from the Makkans. An example would be when the Makkans conducted the public crucifixion of the companion of the Prophet Muhammad (peace be upon him), Khubaib bin Adi. These would be classified as 'terrorist activities' according to the modern usage of the term. So what does this verse say in this context? "Fight in the cause of God those who fight you", "unless they (first) fight you there" - the context of this verse applies to those who initiate the attack against Muslims. And even after they attack, the verse makes it clear: "But if they cease, God is Oft-Forgiving, Most Merciful." And it also makes clear the purpose for what Muslims fight: "fight them on until there is no more tumult or oppression, and there prevail justice and faith in God". It is the duty of Muslims to defend humanity from oppression and persecution and to establish justice. Muslims believe that God has placed us here on earth as his deputy or viceroy, and thus, it is our duty to enjoin the good and forbid the evil, to establish peace and justice in the land. Dr. Maher Hathout writes the following on verses 2:190-194:

These verses were applicable to a particular situation or if, hypothetically, the same situation was to be repeated… Historically, fighting back against the aggressors was prohibited during the thirteen years of the Meccan period. After the migration to Medina and the establishment of the Islamic state, Muslims were concerned with how to defend themselves against aggression from their enemies. The aforementioned verses were revealed to enable them to protect the newly formed state by fighting in self-defence against those who fought them. However, the Qur’an clearly prohibits aggression. The verses explain that fighting is only for self-defence. Thus, a Muslim cannot commit aggression and kill innocent men, women, children, the sick, the elderly, monks, priests, or those who do not wish to fight. A Muslim is also mandated not to destroy plant life of livestock. (Hathout, Jihad vs. Terrorism; US Multimedia Vera International, 2002, p.49, emphasis added)

The historical context is something that must always be considered where developing an understanding of Qur'anic verses. Without knowing the circumstances behind the revelation, one cannot apply the verse as accurately. Shaykh Salman Al-Oadah writes about the general principles in Jihad:

Jihad can never be fought for worldly gain, for conquest, or even for revenge. Muslims must only fight to protect the lives, property, and freedoms of people, especially their freedom to worship Allah when that freedom is forcibly attacked. They are never allowed to attack innocent people, even when they are themselves attacked by the countrymen of those innocents. Any people that go against this established principle of Islamic Law and murder civilians are fighting against Islam and everything that it stands for. It is ludicrous for them to call this fighting a jihâd, a word that means striving in the cause of Islam. They are in fact murderers in the light of Islamic Law and should be treated as such. (SOURCE, emphasis added)

There are strict and detailed laws in Islam, which Muslims must follow carefully. A military Jihad must be performed under these regulations. Abdullah Yusuf Ali writes about verse 2:190:

War is only permissible in self-defence, and under well-defined limits. When undertaken, it must be pushed with vigour, but not relentlessly, but only to restore peace and freedom for the worship of God. In any case strict limits must not be transgressed: women, children, old and infirm men should not be molested, nor trees and crops cut down, nor peace withheld when the enemy comes to terms. (Yusuf Ali, The Holy Qur’an, Text, Translation and Commentary )

He then re-iterates the general principles behind Jihad in his commentary on verse 2:191:

In general, it may be said that Islam is the religion of peace, goodwill, mutual understanding, and good faith. But it will not acquiesce in wrong-doing, and its men will hold their lives cheap in defence of honour, justice, and the religion which they hold sacred. Their ideal is that of heroic virtue combined with unselfish gentleness and tenderness, such as is exemplified in the life of the Apostle. They believe in courage, obedience, discipline, duty, and a constant striving by all the means in their power, physical, moral, intellectual, and spiritual, for the establishment of truth and righteousness. (Yusuf Ali, The Holy Qur’an, Text, Translation and Commentary )

This is the true focus behind Jihad, and Muslims must never lose this focus. Jihad is solely for the purpose of aiding humanity and bringing justice and freedom to the oppressed. Therefore, all actions must be in-line with this focus and the strict regulations governing Jihad. The focus is to defend, not destroy. One who focuses on the betterment and aid of humanity will realize that destruction will never achieve this. Abdul Majid Daryabadi writes extensively on verse 2:190:

2:190 “And fight in the way of Allah those who fight you” – Violating the truce they themselves had signed. The Muslims, after having borne untold persecution with almost superhuman fortitude for years and years at the hands of the pagans of Makkah, are now for the first time enjoined to take to reprisals. ‘For a full thirteen years the Muslims were subjected to relentless persecution in Mecca. The Prophet and his followers fled for life to Medina, but the enemy would not leave them alone in their refuge. They came to attack them within a year, and the first three battles were fought in the very locality which will whether the Prophet was an assailant or defendant’ (Headley, The Original Church of Jesus Christ and Islam, p. 155). The Makkans had signed a truce and were the first to break it. The words ‘fight with those who fight you’ clearly show, firstly, that the Muslims were not the aggressors, and secondly, that those of the enemy who were not actual combatants – children, women, monks, hermits, the aged and the infirm, the maimed, and the like – had nothing at all to fear from the Muslim soldiery. It was in light of this express Divine injunction that the great Abu Bakr, the first Caliph, charged his troops into Syria, ‘not to mutilate the dead, nor to slay old men, women, and children, nor to cut down fruit-trees, nor to kill cattle unless they were needed for food; and these humane precepts served like a code of laws of war during the career of Mohammadan conquest.’ (Bosworth Smith, Mohammed and Mohammedanism, p. 185). Has not Islam thus, in prescribing war against those who break God’s law, who challenge His righteous authority, and who fill the world with violence and injustice, made every concession short of the impossible? Has any code of military ethics been so chivalrous, so humane and so tender towards the enemy? ‘The moral tone adopted by the Caliph Abu Bakr, in his instructions to the Syrian army, was’, says a modern Christian historian, ‘so unlike the principles of the Roman government, that it must have commanded profound attention from a subject people. Such a proclamation announced to Jews and Christians’ sentiments of justice and principles of toleration which neither Roman emperors nor orthodox bishops had ever adopted as the rule of their conduct’ (Finlay, Greece Under the Romans, pp. 367-368). (Daryabadi, The Glorious Qur’an, emphasis added)

Muhammad Asad explains verse 2:190 in the following manner:

This and the following verses lay down unequivocally that only self-defence (in the widest sense of the word) makes war permissible for Muslims. Most of the commentators agree in that the expression la ta'tadu signifies, in this context, "do not commit aggression"; while by al-mu'tadin "those who commit aggression" are meant. The defensive character of a fight "in God's cause" - that is, in the cause of the ethical principles ordained by God - is, moreover, self-evident in the reference to "those who wage war against you", and has been still further clarified in 22: 39 - "permission [to fight] is given to those against whom war is being wrongfully waged" - which, according to all available Traditions, constitutes the earliest (and therefore fundamental) Quranic reference to the question of jihad, or holy war (see Tabari and Ibn Kathir in their commentaries on 22: 39). That this early, fundamental principle of self-defence as the only possible justification of war has been maintained throughout the Quran is evident from 60: 8, as well as from the concluding sentence of 4: 91, both of which belong to a later period than the above verse. (Asad, The Message of the Qur’an, emphasis added)

And on verse 2:191, he states the following:

In view of the preceding ordinance, the injunction "slay them wherever you may come upon them" is valid only within the context of hostilities already in progress (Razi), on the understanding that "those who wage war against you" are the aggressors or oppressors (a war of liberation being a war "in God's cause"). The translation, in this context, of fitnah as "oppression" is justified by the application of this term to any affliction which may cause man to go astray and to lose his faith in spiritual values (cf. Lisan al-Arab). (Asad, The Message of the Qur’an, emphasis added)

This extensive commentary on this verse should sufficiently address all confusion and misconceptions that resulted from misquoting this verse.

Quran 2:216 "Fighting is ordained for you..."

Quran 2:216 Jihad ['Qital'] (holy war in the cause of God) is ordained for you (Muslims), though you dislike it. But it is possible that you dislike a thing which is good for you, and like a thing which is bad for you. But God knows, and you know not.

كُتِبَ عَلَيْكُمُ الْقِتَالُ وَهُوَ كُرْ‌هٌ لَّكُمْ ۖ وَعَسَىٰ أَن تَكْرَ‌هُوا شَيْئًا وَهُوَ خَيْرٌ‌ لَّكُمْ ۖ وَعَسَىٰ أَن تُحِبُّوا شَيْئًا وَهُوَ شَرٌّ‌ لَّكُمْ ۗ وَاللَّـهُ يَعْلَمُ وَأَنتُمْ لَا تَعْلَمُونَ ﴿٢١٦﴾

The first mistake in this translation is that this Quranic verse actually does not use the word “Jihad”. This verse actually uses the word “Qital”, which refers to physical combat in war. Combat is ordained for Muslims in order to defend themselves and their rights, as well as the rights of others. The obligation to physically defend one’s rights, and to establish justice was elaborated on in the previously mentioned article on Jihad. It is sufficient to quote a verse from the Quran in this regard:

4:75 And what is wrong with you that you do not engage in combat for the sake of  Allah, and for those weak, ill-treated and oppressed among men, women, and children, whose cry is: "Our Lord! Rescue us from this town whose people are oppressors; and raise for us from You one who will protect, and raise for us from You one who will help."

وَمَا لَكُمْ لَا تُقَاتِلُونَ فِي سَبِيلِ اللَّـهِ وَالْمُسْتَضْعَفِينَ مِنَ الرِّ‌جَالِ وَالنِّسَاءِ وَالْوِلْدَانِ الَّذِينَ يَقُولُونَ رَ‌بَّنَا أَخْرِ‌جْنَا مِنْ هَـٰذِهِ الْقَرْ‌يَةِ الظَّالِمِ أَهْلُهَا وَاجْعَل لَّنَا مِن لَّدُنكَ وَلِيًّا وَاجْعَل لَّنَا مِن لَّدُنكَ نَصِيرً‌ا ﴿٧٥﴾

It is most certainly a duty of all human beings to help each other from oppression and injustice. This is what Islam teaches. Commenting on verse 2:216, Abdullah Yusuf Ali writes:

To fight (combat) in the cause of Truth is one of the highest forms of charity. What can you offer that is more precious than your own life? But here again the limitations come in. If you are a mere brawler, or a selfish aggressive person, or a vainglorious bully, you deserve the highest censure. (Yusuf Ali, The Holy Qur'an, Text, Translation and Commentary )

Therefore, the fighting ordained by God in the Qur'an is the fighting to establish justice and security in the land, and this is a duty upon all human beings. We will always hope for peace, but we must realize that without justice, freedom, rights and equity, peace will never be able to survive. Likewise, on verse 2:216, Abdul Majid Daryabadi writes:

War, it has been truly said, is sanctioned by the law of nature – the constitution of man and the constitution of society – and is at times a biological and sociological necessity. Islam, the ideal and practical religion has allowed it, but only in cases of sheer necessity. (Daryabadi, The Glorious Qur’an, emphasis added)

Islam has designated war as the last resort and only in cases of sheer necessity, in order for us to defend the rights of ourselves and others. Also, the picture becomes even more clear when we take into consideration the historical context of the revelation. Abdullah Yusuf Ali goes on to explain the historical context in his commentary on verse 2:217:

The intolerance and persecution of the Pagan clique at Mecca caused untold hardships to the holy Messenger of Islam and his early disciples. They bore all with meekness and long-suffering patience until the holy one permitted them to take up arms in self-defence… (Yusuf Ali, The Holy Qur'an, Text, Translation and Commentary )

In light of the above quote, it becomes apparent that fighting has been especially ordained in conditions of severe persecution and hardship. Consequently, the Muslims are required to defend themselves from oppression and establish justice. To abstain from helping those under oppression is cowardice. Abdul Majid Daryabadi also explains the historical context of the verse:

Persecuted, harassed, afflicted, poverty-ridden, exiled, and small in number as the Muslims were at the time of the enactment of warfare, it was but natural that they were none too fond of crossing swords with the mighty forces that had conspired for their extirpation. Nothing short of express and emphatic Divine Command could urge them on to the field of battle [in order to defend their rights]. And yet the Islamic jihads are declared to be ‘designed by the Prophet to satisfy his discontented adherents by an accession of plunder!’ (Margoliouth). Such is this European scholar’s love of veracity! Such is his wonderful reading of history! (Daryabadi, The Glorious Qur’an)

The commentary on this verse makes it very clear that Muslims have always understood this verse as the legal right to defend one’s rights from the forces of oppression, but never to transgress limits .

Quran 4:89 - But if they turn away, catch and slaughter them...

But if they turn away, catch them and slaughter them wherever ye find them; and (in any case) take no friends or helpers from their ranks." (4:89)

This verse has been misquoted like the previous verse, out of context. Here is the full passage:

فَمَا لَكُمْ فِي الْمُنَافِقِينَ فِئَتَيْنِ وَاللَّـهُ أَرْ‌كَسَهُم بِمَا كَسَبُوا ۚ أَتُرِ‌يدُونَ أَن تَهْدُوا مَنْ أَضَلَّ اللَّـهُ ۖ وَمَن يُضْلِلِ اللَّـهُ فَلَن تَجِدَ لَهُ سَبِيلًا ﴿٨٨﴾ وَدُّوا لَوْ تَكْفُرُ‌ونَ كَمَا كَفَرُ‌وا فَتَكُونُونَ سَوَاءً ۖ فَلَا تَتَّخِذُوا مِنْهُمْ أَوْلِيَاءَ حَتَّىٰ يُهَاجِرُ‌وا فِي سَبِيلِ اللَّـهِ ۚ فَإِن تَوَلَّوْا فَخُذُوهُمْ وَاقْتُلُوهُمْ حَيْثُ وَجَدتُّمُوهُمْ ۖ وَلَا تَتَّخِذُوا مِنْهُمْ وَلِيًّا وَلَا نَصِيرً‌ا ﴿٨٩﴾ إِلَّا الَّذِينَ يَصِلُونَ إِلَىٰ قَوْمٍ بَيْنَكُمْ وَبَيْنَهُم مِّيثَاقٌ أَوْ جَاءُوكُمْ حَصِرَ‌تْ صُدُورُ‌هُمْ أَن يُقَاتِلُوكُمْ أَوْ يُقَاتِلُوا قَوْمَهُمْ ۚ وَلَوْ شَاءَ اللَّـهُ لَسَلَّطَهُمْ عَلَيْكُمْ فَلَقَاتَلُوكُمْ ۚ فَإِنِ اعْتَزَلُوكُمْ فَلَمْ يُقَاتِلُوكُمْ وَأَلْقَوْا إِلَيْكُمُ السَّلَمَ فَمَا جَعَلَ اللَّـهُ لَكُمْ عَلَيْهِمْ سَبِيلًا ﴿٩٠﴾ سَتَجِدُونَ آخَرِ‌ينَ يُرِ‌يدُونَ أَن يَأْمَنُوكُمْ وَيَأْمَنُوا قَوْمَهُمْ كُلَّ مَا رُ‌دُّوا إِلَى الْفِتْنَةِ أُرْ‌كِسُوا فِيهَا ۚ فَإِن لَّمْ يَعْتَزِلُوكُمْ وَيُلْقُوا إِلَيْكُمُ السَّلَمَ وَيَكُفُّوا أَيْدِيَهُمْ فَخُذُوهُمْ وَاقْتُلُوهُمْ حَيْثُ ثَقِفْتُمُوهُمْ ۚ وَأُولَـٰئِكُمْ جَعَلْنَا لَكُمْ عَلَيْهِمْ سُلْطَانًا مُّبِينًا ﴿٩١﴾

4:88-91 Why should ye be divided into two parties about the Hypocrites? Allah hath upset them for their (evil) deeds. Would ye guide those whom Allah hath thrown out of the Way? For those whom Allah hath thrown out of the Way, never shalt thou find the Way. They but wish that ye should reject Faith, as they do, and thus be on the same footing (as they): so take not friends from their ranks until they forsake the domain of evil in the way of God (from what is forbidden). But if they revert to [open] enmity, seize them and slay them wherever ye find them; and (in any case) take no friends or helpers from their ranks. Except those who join a group between whom and you there is a treaty (Of peace), or those who approach you with hearts restraining them from fighting you as well as fighting their own people. If God had pleased, He could have given them power over you, and they would have fought you: therefore if they withdraw from you but fight you not, and (instead) send you (guarantees of) peace, then God hath opened no way for you (to war against them). Others you will find that wish to gain your confidence as well as that of their people: every time they are sent back to temptation, they succumb thereto; if they withdraw not from you nor give you (guarantees) of peace besides restraining their hands, seize them and slay them wherever ye get them; in their case We have provided you with a clear argument against them

So in the same manner as the first verse, this verse also only commands Muslims to fight those who practice oppression or persecution, or attack the Muslims. And in the event of a battle, the same laws of war are in place and a Muslim who transgresses limits should prepare for the punishment of God. In response to a question on verses 4:88-89, Dr. Muzammil H. Siddiqi quotes the verses in their full context and then asks the following:

Now tell me honestly, do these verses give a free permission to kill any one anywhere? These verses were revealed by God to Prophet Muhammad (peace and blessings be upon him), at the time when Muslims were attacked by the non-Muslims of Makkah on a regular basis. They were frightening the Muslim community of Madinah. One may say using the contemporary jargon that there were constant terrorist attacks on Madinah and in this situation Muslims were given permission to fight back the “terrorist”. These verses are not a permission for “terrorism” but they are a warning against the “terrorists.” But even in these warnings you can see how much restraint and care is emphasized. (SOURCE, emphasis added)

It is also important to note that the Qur'an clearly condemns murder. The Qur’an says about the prohibition of murder,

6:151 Take not life, which God hath made sacred, except by way of justice and law: thus does He command you, that ye may learn wisdom. 17:33 Nor take life, which God has made sacred, except for just cause. And if anyone is slain wrongfully, We have given his heir authority (to demand Qisas(retribution) or to forgive): but let him not exceed bounds in the matter of taking life; for he is helped (by the law) 5:32...if any one slew a person - unless it be for murder or for spreading mischief in the land - it would be as if he slew the whole people: and if any one saved a life, it would be as if he saved the life of the whole people

So the Qur'an makes it very clear that Muslims cannot initiate an attack against others, unless there is an immediate threat of being attacked. The context of the quoted verses applies only to situations where the oppressors are killing Muslims. In this case, they have a right to defend themselves and others, especially the weak and oppressed.

Quran 5:51 Don't take Jews and the Christians as friends ?!

5:51 O ye who believe! take not the Jews and the Christians for your friends: They are but friends to each other. And he amongst you that turns to them is of them. Verily Allah guideth not a people unjust.

يَا أَيُّهَا الَّذِينَ آمَنُوا لَا تَتَّخِذُوا الْيَهُودَ وَالنَّصَارَ‌ىٰ أَوْلِيَاءَ ۘ بَعْضُهُمْ أَوْلِيَاءُ بَعْضٍ ۚ وَمَن يَتَوَلَّهُم مِّنكُمْ فَإِنَّهُ مِنْهُمْ ۗ إِنَّ اللَّـهَ لَا يَهْدِي الْقَوْمَ الظَّالِمِينَ ﴿٥١﴾

The first point to be noted is that, in the verse above, the word Awliya is often incorrectly translated as friends (Awliya is the plural and its singular is wali and the concept is walaah). As a result, many people are under the misconception that this verse commands Muslims to distance themselves from Non-Muslims and to avoid friendship with them. This is far from the truth, as we shall see after examining the meaning of the word Awliya.God in the  Qur'an says: 

[42:9] 

Or have they taken Awliya besides him? But Allah - He is the wali, and He gives life to the dead, and He is over all things competent.

أَمِ اتَّخَذُوا مِن دُونِهِ أَوْلِيَاءَ ۖ فَاللَّـهُ هُوَ الْوَلِيُّ وَهُوَ يُحْيِي الْمَوْتَىٰ وَهُوَ عَلَىٰ كُلِّ شَيْءٍ قَدِيرٌ‌ ﴿٩﴾ 

3:122 ...Allah was their WALI (protector), and in Allah should the faithful (Ever) put their trust.

وَاللَّـهُ وَلِيُّهُمَا ۗ وَعَلَى اللَّـهِ فَلْيَتَوَكَّلِ الْمُؤْمِنُونَ ﴿١٢٢﴾

This verse indicates that a wali is one in whom trust is placed for protection, as the Qur'an always declares God the protector, wali, of the righteous. As Dr. Saeed Ismail Sieny concludes his discussion on Walaah by writing:

As we have discovered above, the root of the word "al-walaah" does not include love, support, etc., and that the core meaning rests on guardianship. (Sieny, The Relationship Between Muslims and Non-Muslims; Toronto, Al-Attique Publishers Inc., 2000, p. 102, emphasis added)

And Dr. Muzammil Siddiqi writes:

In the verse you quoted, the word "Awliya" is used. It is a plural and its singular is "wali". The correct translation of the word ""wali"" is not "friend" but it is someone who is very close and intimate. It is also used to mean "guardian, protector, patron, lord and master". In the Qur'an this word is used for God, such as “Allah is the Protector (or Lord and Master) of those who believe. He takes them out from the depths of darkness to light…” (Al- Baqarah: 257)

اللَّـهُ وَلِيُّ الَّذِينَ آمَنُوا يُخْرِ‌جُهُم مِّنَ الظُّلُمَاتِ إِلَى النُّورِ‌ ۖ ... ﴿٢٥٧﴾

There are many other references in the Qur'an that give this meaning. The same word is also sometimes used in the Qur'an for human beings, such as
“And whosoever is killed unjustly, We have granted his next kin "wali" the authority (to seek judgment or punishment in this case)…”(Al-‘Isra' :33)
(SOURCE emphasis added)

وَمَن قُتِلَ مَظْلُومًا فَقَدْ جَعَلْنَا لِوَلِيِّهِ سُلْطَانًا فَلَا يُسْرِ‌ف فِّي الْقَتْلِ ۖ إِنَّهُ كَانَ مَنصُورً‌ا ﴿٣٣﴾

It becomes clear that the word Awliya cannot be taken as simply referring to friendship, as it contains a much more complex meaning, including dependence and guardianship. Therefore, a more accurate translation of the verse would be:

5:51 O ye who believe! take not the Jews and the Christians for your protectors: They are but protectors to each other. And he amongst you that turns to them is of them. Verily Allah guideth not a people unjust.

Therefore, the referred verse does not prohibit friendship with Non-Muslims at all. Dr. Muzammil Siddiqi writes:

The Qur'an does not say that non-Muslims cannot be Muslims' friends, nor does it forbid Muslims to be friendly to non-Muslims. There are many non-Muslims who are good friends of Muslim individuals and the Muslim community. There are also many good Muslims who truly and sincerely observe their faith and are very friendly to many non-Muslims at the same time. Islam teaches us that we should be friendly to all people. Islam teaches us that we should deal even with our enemies with justice and fairness. Allah says in the Qur'an in the beginning of the same Surah Al-Ma’dah: “O you who believe! Stand out firmly for Allah as witnesses to fair dealings and let not the hatred of others to you make you swerve to wrong and depart from justice. Be just, that is next to piety. Fear Allah, indeed Allah is well-acquainted with all that you do.” (Al-Ma’dah :8)
In another place in the Qur'an, Allah Almighty says:
“Allah forbids you not with regard to those who fight you not for your faith, nor drive you out of your homes, from dealing kindly and justly with them. For Allah loves those who are just. Allah only forbids you with regard to those who fight you for your faith, and drive you out of your homes and support others in driving you out, from turning to them for protection (or taking them as wali). Those who seek their protection they are indeed wrong- doers.” (Al-Mumtahinah: 8-9)

لَّا يَنْهَاكُمُ اللَّـهُ عَنِ الَّذِينَ لَمْ يُقَاتِلُوكُمْ فِي الدِّينِ وَلَمْ يُخْرِ‌جُوكُم مِّن دِيَارِ‌كُمْ أَن تَبَرُّ‌وهُمْ وَتُقْسِطُوا إِلَيْهِمْ ۚ إِنَّ اللَّـهَ يُحِبُّ الْمُقْسِطِينَ ﴿٨﴾ إِنَّمَا يَنْهَاكُمُ اللَّـهُ عَنِ الَّذِينَ قَاتَلُوكُمْ فِي الدِّينِ وَأَخْرَ‌جُوكُم مِّن دِيَارِ‌كُمْ وَظَاهَرُ‌وا عَلَىٰ إِخْرَ‌اجِكُمْ أَن تَوَلَّوْهُمْ ۚ وَمَن يَتَوَلَّهُمْ فَأُولَـٰئِكَ هُمُ الظَّالِمُونَ ﴿٩﴾

Moreover, Allah Almighty has described Prophet Muhammad, peace and blessings be upon him, as "a mercy" to the worlds. He was a sign of Allah's Mercy to all, Muslims as well as non-Muslims. In his kindness and fair treatment he did not make any difference between the believers and non-believers. He was kind to the pagans of Makkah and fought them only when they fought him. He made treaties with the Jews of Madinah and honored the treaties until they broke them. He, peace and blessings be upon him, is reported to have received the Christians of Najran with kindness in his Masjid in Madinah. They argued with him about Islam, but he returned them with honor and respect. There are many examples from his life that show that he was the friendliest person to all people. (SOURCE)

And as Muhammad Asad writes:

As regards the meaning of the "alliance" referred to here, see 3:28, and more particularly 4: 139 and the corresponding note, which explains the reference to a believer's loss of his moral identity if he imitates the way of life of, or-in Qur'anic terminology-"allies himself" with, non-Muslims. However, as has been made abundantly clear in 60: 7-9 (and implied in verse 57 of this Surah), this prohibition of a "moral alliance" with non-Muslims does not constitute an injunction against normal, friendly relations with such of them as are well-disposed towards Muslims. It should be borne in mind that the term wall has several shades of meaning: "ally", "friend", "helper", "protector", etc. The choice of the particular term - and sometimes a -combination of two terms-is always dependent on the context. (Asad, The Message of the Qur’an, emphasis added)

The second point to note is that although this verse makes a general statement, the ruling is specific and is to be applied in a context similar to the historical context. Shaykh Yusuf Al-Qaradawi wrote about this topic extensively in response to a similar question:

[The answer to this is that these verses are not unconditional, to be applied to every Jew, Christian, or non-Muslim. Interpreting them in this manner contradicts the injunctions of the Qur'an which enjoin affection and kindness to the good and peace-loving peoples of every religion, as well as the verses which permit marriage to the women of the People of the Book, with all that Allah says concerning marriage and He has put love and mercy between you” (30:21)
and the verse concerning the Christians:
And thou wilt find those who say, 'Surely we are Christians,' to be nearest to them (the Muslims in affection...(5:82)
The verses cited above [verse 5:51] were revealed in connection with those people who were hostile to Islam and made war upon the Muslims. Accordingly, it is not permissible for the Muslims to support or assist them - that is, to be their ally- nor to entrust them with secrets at the expense of his own religion and community. This point is explained in other verses, in which Allah, The Most High, says:
They will spare nothing to ruin you; they yearn for what makes you suffer. Hatred has been expressed by their mouths, but what their hearts conceal is still greater. Thus have We made clear to you the revelations (or signs), if you possess understanding. Ah! You love them, but they do not love you…(3:118-119)
This ayah throws light on the character of such people, who conceal great enmity and hatred against the Muslims in their hearts and whose tongues express some of the effects of such hostility. (Al-Qaradawi, Al-Halal Wal Haram Fil Islam; US American Trust Publications, 1994, p. 340, emphasis added)

As Shaykh Qaradawi mentioned, verse 5:11 cannot possibly be taken as a prohibition of friendship since the Qur’an allows Muslim men to marry women from the People of the Book:

5:5 … virtuous women of the believers and the virtuous women of those who received the Scripture before you are lawful for you…

And the Qur’an describes the relationship of marriage to be a relationship with the deepest bond of love:

30:21 And among His Signs is this, that He created for you mates from among yourselves, that ye may dwell in tranquility with them, and He has put love and mercy between your (hearts): verily in that are Signs for those who reflect.

Also note that the Qur’an says:

60:8-9 Allah does not forbid you respecting those who have not made war against you on account of [your] religion, and have not driven you forth from your homes, that you show “Birr” with them and deal with them justly; surely Allah loves the doers of justice. Allah only forbids you respecting those who made war upon you on account of [your] religion, and drove you forth from your homes and backed up [others] in your expulsion, that you make friends with them, and whoever makes friends with them, these are the unjust.

The word “birr” is the same word used to describe a Muslim’s relationship with their parents which is considered the most sacred blood relationship in Islam. Therefore, Muslims are clearly commanded to deal with peaceful non-Muslims is a friendly and peaceful manner. The third point is that the specific groups being referred to in this verse were those hostile to Islam, and not all Jews and Christians in general. Concerning the historical context, the verse was revealed during a time when the Muslims were being attacked from many directions, including the Christian Roman empire and the Jews of Madinah. The Muslims had originally made a pact with the Jews of Madinah, but they were betrayed twice. So in this context, the Qur'an was telling the believers to be cautious in dealings with such enemies who oppose Islam, and not to trust them as protectors. As Jasser Auda writes:

It was revealed in certain historic circumstances, in which there was a war between the infant Islamic state on different occasions on four different fronts: the Romans, the Persians, the pagans of Arabia, and the Jews of Madinah. So, the historic context of the revelation of this verse is a situation of war between Muslims and the People of the Book (Jews, internally in Madinah, and Christians, through a Roman crusade). So, yes, Muslims were not allowed to make friends with the enemies who were fighting them and wishing to eliminate them from the face of the earth. Some Muslims say that since the verse has this historic context, then it is part of history and no longer applies. This is not correct! It is true that the verse has a history behind it, but this does not mean that it is no longer relevant. It is totally relevant but only in a context similar to the historic context. So today Muslims are not to make friends with Jews or Christians (or followers of any other religion for that matter) if they try to kill Muslims, kick them out of their homes, etc. (SOURCE)

The Qur'anic verse is relevant in a similar context to the historical context. A Muslim cannot take Jews or Christians or anyone as protectors if they oppose their religion and its teachings. The Muslims are encouraged to rely on each other for support. Dr. Muzammil Siddiqi writes:

It is obvious that Jews patronize the Jews and Christians patronize the Christians, so why not Muslims patronize Muslims and support their own people. This verse is not telling us to be against Jews or Christians, but it is telling us that we should take care of our own people and we must support each other. In his Tafsir, (Qur’an exegesis) Imam Ibn Kathir has mentioned that some scholars say that this verse (i.e. the one you referred to) was revealed after the Battle of Uhud when Muslims had a set back. At that time, a Muslim from Madinah said, "I am going to live with Jews so I shall be safe in case another attack comes on Madinah." And another person said, "I am going to live with Christians so I shall be safe in case another attack comes on Madinah." So Allah revealed this verse reminding the believers that they should not seek the protection from others, but should protect each other. (See Ibn Kathir, Al-Tafsir, vol. 2, p. 68) (SOURCE)[/

The groups prohibited for Muslims to take as protectors are described in the Qur’an:

The Holy Qur'an, 60:1 O ye who believe! Take not my enemies and yours as protectors,- offering them (your) love, even though they have rejected the Truth that has come to you, and have (on the contrary) driven out the Prophet and yourselves (from your homes), (simply) because ye believe in Allah your Lord! If ye have come out to strive in My Way and to seek My Good Pleasure, (take them not as friends), holding secret converse of love (and friendship) with them: for I know full well all that ye conceal and all that ye reveal. And any of you that does this has strayed from the Straight Path. 60:2 If they were to get the better of you, they would behave to you as enemies, and stretch forth their hands and their tongues against you for evil: and they desire that ye should reject the Truth.

يَا أَيُّهَا الَّذِينَ آمَنُوا لَا تَتَّخِذُوا عَدُوِّي وَعَدُوَّكُمْ أَوْلِيَاءَ تُلْقُونَ إِلَيْهِم بِالْمَوَدَّةِ وَقَدْ كَفَرُ‌وا بِمَا جَاءَكُم مِّنَ الْحَقِّ يُخْرِ‌جُونَ الرَّ‌سُولَ وَإِيَّاكُمْ ۙ أَن تُؤْمِنُوا بِاللَّـهِ رَ‌بِّكُمْ إِن كُنتُمْ خَرَ‌جْتُمْ جِهَادًا فِي سَبِيلِي وَابْتِغَاءَ مَرْ‌ضَاتِي ۚ تُسِرُّ‌ونَ إِلَيْهِم بِالْمَوَدَّةِ وَأَنَا أَعْلَمُ بِمَا أَخْفَيْتُمْ وَمَا أَعْلَنتُمْ ۚ وَمَن يَفْعَلْهُ مِنكُمْ فَقَدْ ضَلَّ سَوَاءَ السَّبِيلِ ﴿١﴾

So the Qur'an forbids taking those as protectors who expel the Muslims from their homes and who would betray and attack as soon as the opportunity arises. Those who have no respect for a Muslim’s beliefs and desire that the Muslim leaves their faith - they cannot be taken as protectors. This is the correct interpretation based on the context of the verse. To conclude, we once again quote Dr. Muzammil Siddiqi:

Muslims are allowed to have non-Muslims as friends as long as they keep their own faith and commitment to Islam pure and strong. You are correct in pointing out that a Muslim man is also allowed to marry a Jewish or Christian woman. It is obvious that one marries someone for love and friendship. If friendship between Muslims and Jews or Christians was forbidden, then why would Islam allow a Muslim man to marry a Jew or Christian woman? It is the duty of Muslims to patronize Muslims. They should not patronize any one who is against their faith or who fights their faith, even if they were their fathers and brothers. Allah says: “O you who believe! Take not for protectors (Awliya') your fathers and your brothers if they love unbelief above faith. If any of you do so, they are indeed wrong-doers.” (Al-Tawbah : 23)
In a similar way, the Qur'an also tells Muslims that they should never patronize the non-Muslims against other Muslims. However, if some Muslims do wrong to some non-Muslims, it is Muslim’s duty to help the non-Muslims and save them from oppression . The Prophet, peace and blessings be upon him, said that he himself will defend a Dhimmi living among Muslims to whom injustice is done by Muslims. But Islam also teaches that Muslims should not seek the patronage of non-Muslims against other Muslims. They should try to solve their problems among themselves. (SOURCE)

Islam is a religion of peace and compassion, therefore it requires its adherents to act in the best possible manner to other human beings. Verse 5:51 does not refer to friends, but protectors, and the historical context reveals that this verse prohibits Muslims from seeking the protection and allegiance of those who are hostile to the Islamic faith. It is not a reference to all Non-Muslims, as the scholars of Islam have clarified.

Footnote:

 Can Christians Befriend Non-Christians?:

The answer from www.gotquestions.org:
http://www.gotquestions.org/friendships-unbelievers.html

Quran 9:29 - Fight those who believe not in God nor the Last Day

9:29 Fight those who believe not in God nor the Last Day, nor hold that forbidden which has been forbidden by God and His Apostle, nor acknowledge the religion of truth, [even if they are] of the People of the Book, until they pay the Jizyah with willing submission, and feel themselves subdued.

قَاتِلُوا الَّذِينَ لَا يُؤْمِنُونَ بِاللَّـهِ وَلَا بِالْيَوْمِ الْآخِرِ‌ وَلَا يُحَرِّ‌مُونَ مَا حَرَّ‌مَ اللَّـهُ وَرَ‌سُولُهُ وَلَا يَدِينُونَ دِينَ الْحَقِّ مِنَ الَّذِينَ أُوتُوا الْكِتَابَ حَتَّىٰ يُعْطُوا الْجِزْيَةَ عَن يَدٍ وَهُمْ صَاغِرُ‌ونَ ﴿٢٩﴾

Some people have falsely concluded from verse 9:29, that Muslims are commanded to attack all non-Muslims until they pay money. In fact, such an interpretation is completely false and contradicts authentic Islamic teachings. Commenting on this verse, Shaykh Jalal Abualrub writes:

These Ayat (Quranic verses) stress the necessity of fighting against the People of the Scripture, but under what conditions? We previously established the fact that the Islamic State is not permitted to attack non-Muslims who are not hostile to Islam, who do not oppress Muslims, or try to convert Muslims by force from their religion, or expel them from their lands, or wage war against them, or prepare for attacks against them. If any of these offenses occurs, however, Muslims are permitted to defend themselves and protect their religion. Muslims are not permitted to attack non-Muslims who signed peace pacts with them, or non-Muslims who live under the protection of the Islamic State. (Abualrub, Holy Wars, Crusades, Jihad)

Likewise, the following fatwa points out that Muslims cannot attack a peaceful non-Muslim country:

Question: Is it an obligation of an Islamic state to attack the neighboring non-Muslim states and collect ‘jizya’ from them? Do we see this in the example of the rightly guided Caliphs who fought against the Roman and Persian Empires without any aggression initiating from them?

Answered by Sheikh Hânî al-Jubayr, judge at the Jeddah Supreme Court

If the non-Muslim country did not attack the Muslim one nor mobilize itself to prevent the practice and spread of Islam, nor transgress against mosques, nor work to oppress the Muslim people in their right to profess their faith and decry unbelief, then it is not for the Muslim country to attack that country. Jihâd of a military nature was only permitted to help Muslims defend their religion and remove oppression from the people.

The Persians and Romans did in fact aggress against Islam and attack the Muslims first.

The Chosroe of Persia had gone so far as to order his commander in Yemen specifically to kill the Prophet (peace be upon him). The Romans mobilized their forces to fight the Prophet (peace be upon him), and the Muslims confronted them in the Battles of Mu’tah and Tabûk during the Prophet's lifetime.

May Allah guide us all. And May peace and blessing be upon our Prophet Muhammad. (SOURCE, emphasis added)

The above fatwa refers to the historical context in which the Prophet Muhammad (peace be upon him) fought against other nations. The Prophet Muhammad did not initiate agression against anyone, rather he and his followers were under attack from all who sought to crush the new Islamic state. The first hostilities between the Muslims and the Roman empire began when the Prophet Muhammad's messenger to the Ghassan tribe (a governate of the Roman empire), Al-Harith bin Umayr Al-Azdi, was tied up and beheaded (Al-Mubarakpuri, Ar-Raheeq Al-Makhtum, p. 383). The killing of a diplomat was an open act of war, and the Prophet Muhammad sent an armed force to confront the tribe, but the Roman empire brought in reinforcements and the resulting conflict, known as the Battle of Mut'ah, was a defeat for the Muslims. Only after this did subsequent battles between the Muslims and the Roman Empire occur, and the Muslims emerged victorious. Likewise, as mentioned in the above fatwa, hostiltiies between the Muslims and the Persians only began after the Persian emperor Chosroe ordered his governor in Yemen Badham, to kill the Prophet Muhammad pbuh, although his efforts were thwarted when the latter accepted Islam. Other non-muslim groups, such as those in Madinah, also initiated hostilities against the Muslims despite peace treaties as Shaykh Sayyid Sabiq writes:

As for fighting the Jews (People of the Scripture), they had conducted a peace pact with the Messenger after he migrated to Madinah. Soon afterwards, they betrayed the peace pact and joined forces with the pagans and the hypocrites against Muslims. They also fought against Muslims during the Battle of A`hzab , then Allah revealed…[and he cites verse 9:29] (Sayyid Sabiq, Fiqhu as-Sunnah, Vol. 3, p. 80)

In light of the historical context of this verse, it becomes very clear that the verse was revealed in connection with agression initiated against Muslims. As Dr. Jamal Badawi very accurately concludes with regard to verse 9:29 and similar verses:

All of these verses, without exception, if studied carefully, address aggression and oppression committed against Muslims at the time of the Prophet (peace and blessings be upon him), whether by idolatrous Arabs, some of the Jewish tribes in Madinah, or by some Christians. (SOURCE)

Therefore, the command to fight in verse 9:29 relates to those non-muslims who commit agression and not those who are committed to live in peace. The verse is subject to certain conditions that were apparent when it was implemented in the time of the Prophet Muhammad pbuh, as Shaykh Sayyid Sabiq writes:

What we have stated makes it clear that Islam did not allow the initiating of hostilities, except to: 1. repel aggression; 2. protect Islamic propagation; 3. deter Fitnah and oppression and ensure freedom of religion. In such cases, fighting becomes a necessity of the religion and one of its sacred ordainments. It is then called, ‘Jihad’. (Sayyid Sabiq, Fiqhu as-Sunnah, Vol. 3, p. 81)

The verse then proceeds to mention some issues relating to the Islamic state, and governing non-muslim citizens of the Islamic state. Dr. Maher Hathout comments on the regulations in verse 9:29:

Freedom of religion is an essential aspect in an Islamic state. One of the five pillars of Islam is zakat (almsgiving). The People of the Book (Christians and Jews) are not obliged to pay the Islamic zakat that is spent by the state for social necessities and state affairs as defined in the Quran (see 9:60). But they must pay other taxes to share in the state budget. If they refuse to pay this tax to the state and rebel against the state, then it is the obligation of the state to confront them until they pay it. This is what Caliph Abu Bakr did after the death of the Prophet, when some people refused to pay zakat. (Hathout, Jihad vs. Terrorism; US Multimedia Vera International, 2002, p.53)

The verse mentions Jizya, which is unfortunately misunderstood by some people. Like any nation, the Islamic government requires its citizens to pay taxes in return for its services. Since Muslims pay the Zakat, the non-muslim citizens are required to pay Jizya (for more information on Jizya, please refer to Jizya in Islam and Jizyah and non-muslim minorities). Dr. Monqiz As-Saqqar writes concerning the Jizya tax:

The sum of jizya was never large to the extent that the men were unable to pay. Rather, it was always available and reasonable. During the reign of the Prophet, peace and blessings be upon him, jizya never exceeded one dinar annually and it never exceeded four dinars under the Umayyad rule. (SOURCE)

Shaykh Abu'l-Hasan Al-Mawardi (d. 1058CE) explicitly points out that the Jizya should be exacted in accordance with the means of the people, and the Imam should judge the conclude the amount to the satisfaction of the leaders of those being taxed:

The fuqaha (Jurists) differ as to the amount of the Jizya. Abu Hanifa considers that those subject to this tax are of three kinds: the rich from whom forty-eight dirhams are taken; those of average means from whom twenty four are taken, and the poor from whom twelve dirhams are taken: he thus stipulated the minimum and maximum amounts and prohibits any further judgement on behalf of those responsible for its collection. Malik, however, does not fix its minimum and maximum amount and considers that those responsible should make their own judgement as to the minimum and maximum. Ash-Shafi'i considers that the minimum is a dinar, and that it is not permitted to go below this while he does not stipulate the maximum, the latter being dependant on the ijtihad (judgement) of those responsible: the Imam, however, should try to harmonise between the different amounts, or to exact an amount in accordance with people's means. If he has used his judgement to conclude the contract od jizyah to the satisfaction of the leaders of the people being taxed, then it becomes binding on all of them and their descendants, generation after generation, and a leader may not afterwards change this amunt, be it to decrease it or increase it. (Al-Mawardi, al-Ahkam as-Sultaniyyah, Ta-Ha Publishers Ltd. 1996, pp. 209-210)

Hence, the laws of Islam forbid Muslims from opressing non-muslims and command them to treat others with justice and compassion. In fact, the Prophet Muhammad pbuh himself forbade Muslims from harming non-muslim citizens of an islamic state or any non-muslim with whom there was an agreement of peace, as he said,

"The one who wrongs a covenanter or impairs his right or overworks him or forcibly takes something from him, I will be his prosecutor on the Day of Judgment. (Sunan Abi Dawud 170/3 no. 3052, Sunan an-Nasa'i 25/8 no. 2749, and verified by Al-Albani no. 2626).

In conclusion, verse 9:29 commands Muslims to fight against only those who initiate agression as illustated by its historical context. Muslims may only fight under strict conditions, and are commanded to live peacefully with peaceful non-muslim neighbors.

Further readings:
http://www.letmeturnthetables.com/2011/05/reality-of-jizya.html 
http://discover-the-truth.com/2014/06/03/examining-quran-929-does-islam-sanction-the-killing-of-christians-and-jews/

Quran 47:4 When you meet the infidels,smite their necks ?!

Qur'an 47:4 So, when you clash with the unbelieving Infidels in battle, smite their necks until you overpower them, killing and wounding many of them. At length, when you have thoroughly subdued them, bind them firmly, making (them) captives. Thereafter either generosity or ransom until the war lays down its burdens. Thus are you commanded by God to continue carrying out Jihad against the unbelieving infidels until they submit to Islam .

Once again a poor translation serves the purpose of the Islam-haters very well. Let us examine a more accurate translation before analyzing the verse:

47:4 Therefore, when ye meet the Unbelievers in battle, smite at their necks; At length, when ye have thoroughly subdued them, bind a bond firmly (on them): thereafter (is the time for) either generosity or ransom: Until the war lays down its burdens. Thus (are ye commanded): but if it had been God's Will, He could certainly have exacted retribution from them (Himself); but (He lets you fight) in order to test you, some with others. But those who are slain in the Way of God,- He will never let their deeds be lost.

فَإِذَا لَقِيتُمُ الَّذِينَ كَفَرُ‌وا فَضَرْ‌بَ الرِّ‌قَابِ حَتَّىٰ إِذَا أَثْخَنتُمُوهُمْ فَشُدُّوا الْوَثَاقَ فَإِمَّا مَنًّا بَعْدُ وَإِمَّا فِدَاءً حَتَّىٰ تَضَعَ الْحَرْ‌بُ أَوْزَارَ‌هَا ۚ ذَٰلِكَ وَلَوْ يَشَاءُ اللَّـهُ لَانتَصَرَ‌ مِنْهُمْ وَلَـٰكِن لِّيَبْلُوَ بَعْضَكُم بِبَعْضٍ ۗ وَالَّذِينَ قُتِلُوا فِي سَبِيلِ اللَّـهِ فَلَن يُضِلَّ أَعْمَالَهُمْ ﴿٤﴾

So we now see some grievous mistakes made in the poor translation quoted. 1. The verse makes NO mention whatsoever of "killing and wounding" 2. "Thus are you commanded by God to continue carrying out Jihad against the unbelieving infidels until they submit to Islam " is a complete addition to the verse and is not found anywhere in the Qur'an! 3. That verse does not use the word Jihad at all It is very clear that the context of this verse is in battle, and when in battle the defenders of humanity should attack the unjust oppressors until they are subdued. Professor Shahul Hameed comments on verse 47:4 by saying:

The context of this verse was when the Muslims were to fight their enemies for their very existence. After thirteen years of endurance and patience, the prophet and his companions had to leave their home town of Makkah and to emigrate to Madinah. When the people of Madinah had welcomed him there and he was accepted as a leader there, the Makkans became unhappy. They wanted to eliminate Muhammad and his religion; and so they sent their army to root out Islam. And the crucial battle took place in Badr. It was just before this that Muhammad received the revelation from God to fight: {And fight in the way of Allah with those who fight with you, and do not exceed the limits, surely Allah does not love those who exceed the limits.} (Al-Baqarah 2:190)
This meant that the Prophet and his companions were not to start the fighting; but to defend themselves against aggressors. That was how fighting was ordained; but we must know that once we fight, we fight to defeat the aggressors, so that we can live without fear of molestation and invasion; so that we can live in peace; so that justice is done. Remember God does not command any one to start fighting; rather He permits people to fight in self defence or for the defence of those who are attacked unjustly. (SOURCE)

The historical context again illustrates a condition of constant struggle and war. In such a condition, God reassures the believers that He is with them, and to therefore have full faith, strength and bravery in battle and not to cower from the enemy. As Abdullah Yusuf Ali writes:

When once the fight (Jihad) is entered upon, carry it out with the utmost vigour… (Yusuf Ali, The Holy Qur'an, Text, Translation and Commentary )

Likewise, Dr. Maher Hathout writes:

Clearly, these verses are applicable in the heat of battle and against an aggressive combating force. (Hathout, Jihad vs. Terrorism; US Multimedia Vera International, 2002, p.49)

Muslims are encouraged to restrain the enemy by capturing them, and to therefore minimize loss of life. Moreover, the verse specifically mentions that Muslims should subdue the enemies "until the war lays down its burdens", i.e. until the enemy stops fighting. Similar to this verse:

8:61 But if the enemy incline towards peace, do thou (also) incline towards peace, and trust in God: for He is One that hears and knows (all things).

وَإِن جَنَحُوا لِلسَّلْمِ فَاجْنَحْ لَهَا وَتَوَكَّلْ عَلَى اللَّـهِ ۚ إِنَّهُ هُوَ السَّمِيعُ الْعَلِيمُ ﴿٦١﴾  

So the verse is very specific, in that it is limited to the context of a battle and the Muslims should only fight until the enemy is subdued or inclines towards peace i.e. they should not transgress limits. In the event of a battle, the verse guides Muslims to abstain from transgressing limits and only to fight the enemy until they are subdued or cease fighting. Shaykh Muhammad Saalih Al-Munajjid comments about the treatment of prisoners:

If the Muslims capture them and take them to a place that has been prepared for them, they should not harm them or torture them with beatings, depriving them of food and water, leaving them out in the sun or the cold, burning them with fire, or putting covers over their mouths, ears and eyes and putting them in cages like animals. Rather they should treat them with kindness and mercy, feed them well and encourage them to enter Islam... ...The Prophet (peace and blessings of Allaah be upon him) used to enjoin the Muslims to treat prisoners well, whereas the Romans and those who came before them the Assyrians and Pharaohs, all used to put out their prisoners’ eyes with hot irons, and flay them alive, feeding their skins to dogs, such that the prisoners preferred death to life. (SOURCE)

Therefore, Islam has laid out clear rules and regulations for Muslims to follow in the event of war, which is only used as a last resort.