Yeah, there is the middle name ... I think beyond that (and most everything that I will mention is either a stereotype or based on some half truth)
1) Many blacks have converted to Islam
2) The 2008 question of where he was born and that it was in an Islamic country (Kenya? forgot where the claim was)
3) He has taken a softer line (at least in the 2008 campaign) on the war on terror that Bush or even Hillary (though he did keep Guantanamo open, etc)
4) Association with some anti-Semitics (Rev. Wright) and a general guilt by association of being a black leader ala Jessie Jackson/Farakahn, et al.
Those things have been half baked into the Obama is a Muslim/pro terrorist.
Like I said, I think he is a total piece of shit President and the ObamaCare roll out is confirming that belief in my mind more and more.
But everyone can relax, he is not a Muslim, he is a regular Church going Christian and thankfully he is less than 4 years away from being an ex-President.