Becky's right, GfS. The issue isn't that Williams's stated opinion was "politically incorrect" but that NPR, as a news source, is supposed to be dealing as much as possible with verifiable facts and objective analysis, not serving as a propaganda outlet for any particular political persuasion.   
I'll bet that if Williams had said something like "When I hear any politician argue that we should raise taxes, in my gut I think of Stalin," or "Whenever I see a white man dressed in an Armani suit and driving a Lexus, I can't help wondering if he's a Wall Street crook," NPR's reaction would have been pretty much the same. It's not WHICH group he's contributing to stereotyping, it's THAT giving vent to such prejudices in a national TV show is not behaving like a responsible news analyst.