After several months now of surfing the web trying to understand the Islamist threat, I have concluded that Little Green Footballs is the single best site for the general reader. It presents the essential facts and best opinion pieces, and does so without any religious overtones. (That's not to say that the editors aren't religious, but that they do a very good job of keeping their personal views out of their commentary). If you have time to only visit one site, I'd recommend that it be LGF.
PS today they point out an interesting article by a Kuwaiti Political Scientist who writes that Muslims bear the responsibility for the West's growing distrust of them. I hope many more people join him in stating such views, including some in our own universities.