I don't think what he said makes him a bigot and based on his discussion alone he should not have been fired. Humans have evolved to identify patterns as a mechanism for self-preservation. (Eg: TV shows us: "ALLAH AKHBAR!!" -> BOMB -> people die -> conditioned to resist Islam in all forms/places in order to survive). Psych 101.
People who claim Islam is a peaceful religion are deluded. The religion is based on the doctrine and the doctrine is full of violent - what we now consider highly immoral - dictations. Islam is also not exclusively violent by any means. This whole meme is a lesson in our susceptibility toward irrational beliefs and using reason to overcome that for our own benefit AND the comfort for our collective living space.
However, if a 27 yr old average-Jake can live amongst Muslims, talk with Muslims, maintain many Muslim friends and identify that the chances of being killed by a terrorist attack in America is less than being struck by lightning, then shame on a middle-aged, highly "intellectual" and "cultured" Juan Williams for not doing the same.
As far as being fired by NPR, well, he was correct to say he does not fit in (their) box. NPR is one of the last bastions of relatively untainted journalism in the current age of admitted anti-intellectualism. It's pretty obvious where the conflict of interest arises when you act as an NPR analyst during the day and a Fox pundit at night, not to mention breaking specific sections of NPR's employee standards regarding making opinions public. If he was fired for any reason other than continually defying this employer statute over the course of years, then his termination was wrong.
This isn't censorship though, it's business. My employer is a DOD contractor and if I go around bad-mouthing the DOD there is a good chance we will lose contracts and I will get fired. I took the job on this understanding of professional discretion. Juan Williams did the same, was indiscrete (many times) and was fired for it.
Well what about cutting federal funding?!?!?!??!?!!?
I think there is an argument to be made that if he was NOT fired then gov't funding should have ceased because these funds were being allocated based on the presumption of set standards (ie. contractual guidelines for employees) that was being consistently stretched and broken over Mr. Williams' tenure.
