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" (2:190-
193).

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 9, verse 5 -- which in its snipped,
out of context version could read: "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)." Again, the preceding and following 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 Oft-
Forgiving, 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."