For a muslim Obama to have a hope of even winning the democratic nomination, you would have to, at the very least, butterfly away 9/11 and all of the radical muslim terrorist incidents, going back to the early 80s. Maybe, if all is nice and mellow between islam, and the western judaeo-christian world, it might be possible, but even then, I doubt it. An earlier poster alluded to Mitt Romney being a mormon. Big strike against him. Many in America think that the mormons are some sort of cult, but at least nobody accuses them of terrorism. And I doubt Romney will ever get the GOP nomination.
Then there is the Jewish question. A moslem POTUS will give Israel a real bad case of the jitters. This will cause America's liberal jewish community much grief, as they desperately want to vote for Obama, but don't want to be disloyal to Israel. Even some African American voters may have problems with his religion. They tend to be devout christians, often fundamentalist at that. As much as they will want to vote for the first black with a real shot at winning, his religion will be a problem for them as well. Most people who don't live in the US don't really understand how a compelling this issue is; about being a born-again christian.
Lastly, Middle America, however you want to define that, just wont be comfortable with the idea. If the nominee were jewish, same thing, and nobody seriously accuses Jews of terrorism either, at least not since the Irgun went away.