I think Richard Dawkins was lying ...
when he said:
I know nothing of any stance [Bill Maher] may have taken on medical questions.
Long post (w/ tons of links) that fleshes out the story here
I suspect that they enjoyed his religion-baiting film and didn't really consider whether he really merited the award.
As scienceblog, to which you linked, put it:
"So what if Maher supports quackery? No problem. As long as he bashes religion, it's all good."
Dawkins is a poor spokesman for atheism. Equating a religious upbringing with child abuse, as I heard him do in an interview on TV, is absurd hyperbole.