Again, I think this 'message' is at the front of your mind and it's biased what you're observing. The Megaton doctor is a good example, why is he an example of a positive individual when he's largely disinterested in people's problems? Why is the head of the town a positive example when he's both the political leader and the head of security? I wouldn't want to live someplace where the head of police was also the mayor.
I think this really says it all - the original poster had to really be Looking for it to see it.
IMHO there is no racism present in any form that could be construed as inappropriate in Fallout 3.
Given that we are in America, if there had been blatant and inappropriate racism put into the game, there would have been a Huge backlash against Bethesda. It doesn't take very much these days to touch of a firestorm of criticism - and we really don't need to try and find racism where it does not exist. I am not surprised that someone tried to pull the racist card, but I also get angry when people do it in situations where there is clearly no racism present.
Ridiculous notion that Fallout 3 is racist - just ridiculous.