As I wrote at Greg's place earlier, Thinkprogress omitted some relevant context from Juan Williams' remarks, but they were hardly, as William Saletan characterized, meant as a repudiation of those feelings, since he told George Stephanopolous that he should have gone on to repudiate them and didn't.
Again, it's hard to have an honest conversation about bigotry if you can't say how you feel in pretty bland terms without getting fired. But the larger context is FOX News' sustained anti-Muslim fearmongering, to the point of bringing on a guy to defend Williams who thinks most religiously observant American Muslims are part of a conspiracy to institute Taliban-style Sharia law. Thinkprogress has been doing a great job documenting that, and I agree with Glenn Greenwald that much of the conservative outrage over Williams' firing has to do with conservatives taking offense at the idea that there's something wrong with anti-Muslim bigotry, as opposed to the honest and contrite expression of same.
I should have said this earlier, but even if you think Williams was wronged, it seems a bit strange to me that the issue is now NPR instead of the fact that FOX News uses its platform to regularly spread fear and disinformation about Muslims and Islam. The 2.5 million American Muslims FOX smears daily aren't getting millions of dollars to give their opinions of current events on television.