Primarily it is for two reasons, his name "Barack Hussein Obama" which is a very muslim name, and the fact that his father is muslim. What's sad is that there is still a fair amount of people out there who still believe he is Muslim, 15% of the people who voted in the WV primary voted against Obama because they believed he was Muslim.
Personally I don't think that it should matter one way or another what religion the candidate is, Christian, Jewish, Muslim, Wiccan, Aethist whatever. We are supposed to have freedom of religion in this country so it simply shouldn't matter.
