This article by Mary Katherine Ham serves as a good resource for getting a handle on the controversy. CAIR, of course, has jumped in, wanting Prager's head (so to speak). I saw Dennis Prager on Hannity and Colmes TV show tonight and if a transcript is made available I'll link to it. Prager did a good job defending his position, though I am personally somewhat ambivalent. (HT: Michelle Malkin)
Update 12/18/06 - Don Feder weighs in for his own reasons. He lists the violence enjoined by the Koran and concludes,
It's no coincidence that most terrorists on four continents are Muslims. Nor is it a coincidence that those who are killing U.S. servicemen in Iraq do so inthe name of the bible of Islam. And it isn't by chance that Osama bin Laden, Hamas, Hezbollah and Imanutjob in Iran all cite the Koran as the source of their lunacy.