The Quran contains at least 109 verses that speak of war with nonbelievers, usually on the basis of their status as non-Muslims. Some are quite graphic, with commands to chop off heads and fingers and kill infidels wherever they may be hiding. Muslims who do not join the fight are called ‘hypocrites’ and warned that Allah will send them to Hell if they do not join the slaughter.
Unlike nearly all of the Old Testament verses of violence, most verses of violence in the Quran are open-ended, meaning that they are not necessarily restrained by historical context contained in the surrounding text (although many Muslims choose to think of them that way). They are part of the eternal, unchanging word of Allah, and just as relevant or subject to interpretation as anything else in the Quran.
The context of violent passages is more ambiguous than might be expected of a perfect book from a loving God. Most contemporary Muslims exercise a personal choice to interpret their holy book’s call to arms according to their own moral preconceptions about justifiable violence. Islam’s apologists cater to these preferences with tenuous arguments that gloss over historical fact and generally don’t stand up to scrutiny. Still, it is important to note that the problem is not bad people, but bad ideology.