Obama may not be a secret Muslim, but apparently Muslims do like him best out of all religious groups (including non-religious people). Relatedly, Mormons apparently like the President the least.
I doubt that's something the President would like to advertise, considering the persistence of rumors claiming him to be a foreign-born Muslim, but it's an interesting fact to consider nonetheless. For one thing, while Obama is pretty popular among Muslim Americans, the same cannot really be said for his image in the Middle East (although it seems likely he's slightly preferred to his predecessor). For another, one might expect Muslims to be somewhat socially conservative and to therefore disapprove of Obama's endorsement of issues like marriage equality or birth control.
There's a few possible reasons for this in my view. First of all, it's important to distinguish between Muslims and Arabs / Middle East (a distinction unfortunately lost on many people). The world's largest Muslim country is not Saudi Arabia or Iraq - it's Indonesia, which is located in Southeast Asia, between Thailand and Australia. So it's possible that Obama's image problem in the Middle East has more to do with cultural/nationalist issues than religious affiliation. In other words, it's the Arab-speaking and Persian-speaking world he has an image issue with, not the Muslim world.
Secondly, the mixing of religion and politics is always a complicated thing. Catholics, by and large (we're speaking in generalities), are also opposed to abortion and gay marriage but nonetheless consistently vote Democratic. This is to a large extent because Democrats have been perceived (since about the 1890s) as the ally of immigrants and religious minorities, which in many cases has purchased the Democratic Party a fair amount of credit. That credit does have its limits - white (conservative) Catholics have been drifting away from the Party for the last decade - but it certainly goes a long way. After all, who would you rather vote for? A politician who agrees with your views on marriage but would like to see you deported or a politician who disagrees with you but promises to protect your residency and right to express your beliefs?
In conclusion, I think this is pretty good news. It indicates, among other things, that Muslim Americans are probably beginning to feel accepted and perhaps even welcomed in American culture. Obviously there are still challenges ahead and Islamophobia is definitely a thing we still have to wrestle with, but I for one am hopeful.