I actually remember looking at a poll in my book from my freshman U.S. Government/Politics class in which the majority of people wouldn't vote for an atheist president. Muslims and gays were pretty low on that graph too.
http://en.wikipedia.org/wiki/Freedom...on_of_atheists The results shown here are close enough.
Religion should not be an issue unless it starts to become public. It is a personal issue, and if your beliefs are getting in the way of your social competence, then there is a problem.