Robert Wright, author of The Evolution of God exegetes the so-called "sword verse," which is used by a lot of Islamic radicals to justify their violence, and a lot of anti-Islamic bigots to justify their hatred of Islam. Here's the key passage:
In short, “kill the polytheists wherever you find them” doesn’t mean “kill the polytheists wherever you find them.” It means “kill the polytheists who aren’t on your side in this particular war.”
Presumably, particular wars were the typical context for the Koran’s martial verses—in which case Muhammad’s exhortations to kill infidels en masse were short-term motivational devices. Indeed, sometimes the violence is explicitly confined to the war’s duration: “When ye encounter the infidels, strike off their heads till ye have made a great slaughter among them, and of the rest make fast the fetters. And afterwards let there either be free dismissals or ransomings, till the war hath laid down its burdens.”
Of course, if you quote the first half of that verse and not the second half—as both jihadists and some western commentators might be tempted to do—this sounds like a death sentence for unbelievers everywhere and forever. The Koran contains a number of such eminently misquotable lines. Repeatedly Muhammad makes a declaration that, in unalloyed form, sounds purely belligerent—and then proceeds to provide the alloy.
It's always an important reminder that texts have contexts, and that a verse plucked from any religious text, divested of both its textual setting and its societal and cultural context can be misleading, both to those who subscribe to the religion, and to those who would wish it ill. Wright does admirable service to deepening our understanding of Islam.