It isn't a matter of intolerance so much as one of "false knowledge." I know lots of real people, and none of them think he's Muslim. The only place "many" think so is on the internet.
There is a lot of mis-information on the internet. Someone puts garbage out there maliciously, and it circulates endlessly. But the only place you get something useful out of piling garbage on top of garbage is a compost heap. For the internet, the old data processing axiom applies. If you are using bad information, the analysis is inherently bad. In other words, "garbage in; garbage out."
People who over-consume the nonsense on the internet without sorting it out may be "intolerant," but they are also sheep being led to a sheering if they fail to think about the "stories" they see on line. That intellectual laziness is nothing other than immature. Intolerance is often a simple failure to understand the reality of the situation.
So those who don't want to vote for Obama because they "think" he is Muslim have a really low threshold for how they define "thinking."