Several websites I've read quote these passages to show that the Qu'ran does not believe in the things the "militant" Muslims do...
"Fight in the cause of Allah against those who fight you, but do not transgress limits. Allah does not love transgressors." (Quran 2:190)
"If they seek peace, then seek you peace. And trust in Allah for He is the One that heareth and knoweth all things." (Quran 8:61)
But if you put them in context, you might see it a bit different.
In Al Baqarah (2):
"O ye who believe! Retaliation is prescribed for you in the matter of the murdered; the freeman for the freeman, and the slave for the slave, and the female for the female. And for him who is forgiven somewhat by his (injured) brother, prosecution according to usage and payment unto him in kindness. This is an alleviation and a mercy from your Lord. He who transgresseth after this will have a painful doom."
And there is life for you in retaliation, O men of understanding, that ye may ward off (evil). (Quran 2:178-179)
In Al Anfaal (8):
"And when those who disbelieve plot against thee to wound thee fatally, or to kill thee or to drive thee forth; they plot, but Allah plotteth; and Allah is the best of plotters." (Quran 8:30)
"And fight them until persecution is no more, and religion is all for Allah. But if they cease, then lo! Allah is Seer of what they do." (Quran 8:39)
And here is the verse before 61, about "seeking peace"...
"Make ready for them all thou canst of force and of horses tethered, that thereby ye may dismay the enemy of Allah and your enemy, and others beside them whom ye know not. Allah knoweth them. Whatsoever ye spend in the way of Allah it will be repaid to you in full, and ye will not be wronged." (Quran 8:60)
I guess it doesn't seem very clear to me. In fact, it reads like much of the Old Testament. Someone mentioned the Crusades, but would a Catholic today march to war on the orders of the Pope? And how many of you Baptists or Methodists would strap up with explosives and hop a plane because your pastor encouraged it?
Seems to me the "fundamentalists" of the western religions shoot doctors and bomb abortion clinics to save the unborn, but are generally spurned by reasonable people. It may simply be easier to gain influence over young, oppressed, poor men in middle eastern cultures... and explain that the Qu'ran expects them to kill people of the "evil empire".