Clive Crook says that
Williams was not expressing hatred or intolerance of Muslims. He was confessing to the kind of anxiety that I suspect many and possibly most Americans feel. (Watch the body language in the departure lounge.) He was acknowledging a sad reality.
No he wasn't acknowledging this sadly; he was justifying it.
He was talking in the context of America having a "Muslim dilemma" in the larger context of Bill O'Reilly's statement that "Muslims killed us on 9/11!" No one would argue that saying that Jihadist terrorism is motivated by extreme Islam, rather than Christianity or Buddhism is bigotry, for Pete's sake. But the notion that every Muslim is therefore guilty before being proven innocent, that those building Park51 have to prove they're not al Qaeda or be deemed Jihadists, that Muslims who wear Muslim garb are rightly suspected of being terrorists on airplanes (even when no actual Jihadist on an airplane has worn such garb) is fanning the flames of bigotry.
Yes, Islamism is related to Islam. But the distinction is critical to winning the war. And tarring all people in Muslim garb as somehow legitimately related to terrorism is, yes, bigotry. And, in general, it's a rule of thumb that anyone who constructs a sentence "I'm not a bigot, but ..." is almost always a bigot.