The Qur'an commands Muslims to stick up for themselves in a defensive battle -i.e. if an enemy army attacks, then Muslims are to fight against that army until they stop their aggression. All of the verses that speak about fighting/war in the Qur'an are in this context. There are some specific verses that are very often "snipped" out of context, either by those trying to malign the faith, or by misguided Muslims themselves who wish to justify their aggressive tactics. For example, one verse (in its snipped version) reads: "slay them wherever you catch them" (Qur'an 2:191). But who is this referring to? Who are "they" that this verse discusses? The preceding and following verses give the correct context: "Fight in the cause of God those who fight you, but do not transgress limits; for God loves not transgressors. And slay them wherever ye catch them, and turn them out from where they have turned you out; for tumult 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, slay them. Such is the reward of those who suppress 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 prevails justice and faith in God; but if they cease, let there be no hostility except to those who practise oppression" (2:190193). It is clear from the context that these verses are discussing a defensive war, when a Muslim community is attacked without reason, oppressed and prevented from practicing their faith. In these circumstances, permission is given to fight back -- but even then Muslims are instructed not to transgress limits, and to cease fighting as soon as the attacker gives up. Even in these circumstances, Muslim are only to fight directly against those who are attacking them, not innocent bystanders or non-combatants. Another similar verse can be found in chapter out of context version could read: "fight and them, and seize them, beleaguer them, and lie (of war)." Again, the preceding and following 9, verse 5 -- which in its snipped, slay the pagans wherever ye find in wait for them in every stratagem verses give the context.
This verse was revealed during a historical period when the small Muslim community had entered into treaties with neighboring tribes (Jewish, Christian, and pagan). Several of the pagan tribes had violated the terms of their treaty, secretly aiding an enemy attack against the Muslim community. The verse directly before this one instructs the Muslims to continue to honor treaties with anyone who has not since betrayed them, because fulfilling agreements is considered a righteous action. Then the verse continues, that those who have violated the terms of the treaty have declared war, so fight them... (as quoted above). Directly after this permission to fight, the same verse continues, "but if they repent, and establish regular prayers and practise regular charity, then open the way for them... for God is Oft-forgiving, Most Merciful." The subsequent verses instruct the Muslims to grant asylum to any member of the pagan tribe/army who asks for it, and again reminds that "as long as these stand true to you, stand ye true to them: for God loves the righteous." Any verse that is quoted out of context misses the whole point of the message of the Qur'an. Nowhere in the Qur'an can be found support for indiscriminate slaughter, the killing of non-combatants, or murder of innocent persons in 'payback' for another people's alleged crimes.
The Islamic teachings on this subject can be summed up in the following verses (Qur'an 60:7-8): "It may be that God will grant love (and friendship) between you and those whom ye (now) hold as enemies. For God has power (over all things), and God is OftForgiving, Most Merciful. God does not forbid you, 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 God loves those who are just."