NPR is supposed to be party-neutral. That's the whole point of it. Yes, it's viewed as a liberal organization, and perhaps it does have a democratic slant (hmmm, a government-sponsored organization that's in favor of increased funding for social programs? Imagine that!), but ideally it should be relatively bias-free, or at least work to balance its bias by presenting both sides of important issues.
Part of that is hiring journalists whose opinions may differ from the opinions of the management, no matter which side of the political spectrum you hail from. If he had been fired because he'd said something unflattering (but true) about a democrat, I would be incensed right now.
But on the other hand, the dude admitted to being subtly racist. I'd have fired him, too, if I thought keeping him on was going to seem to condone or legitimize racial profiling.
I haven't heard the "official reasoning" behind letting him go, but if they're explicitly saying "he's too conservative to work here," then that is wrong, wrong, wrong. If it's "what he said was offensive to Muslims and we no longer wish to employ him," that's a different issue, at least in my mind.
Also, this:
http://muslimswearingthings.tumblr.com/