He didn't get fired because he was african american, he got fired because he wasn't a member of the liberal media cabal at NPR.
RealClearPolitics - Video - Krauthammer Slams NPR's Hypocrisy Over Williams And Totenberg
I have no idea why he got fired. the article I gave was an opinion which I found interesting (from another African American working at NPR), but certainly not definitive. Your link truly says nothing about the reason for the firing.
Sometimes a person just needs firing. Sometimes its not a popular thing to do. I don't know if it was the right decision by NPR, but I would bet there are many reasons behind it.