it doesn't matter that he never was a muslim. if his father was one, the he's automatically regarded as one. And is considered a traitor if he ever chooses a different faith.
Psychologically this will limit Obamas reactions and degrade any efficiency of performing his duties as POTUS by the very fact of being raised a Muslim.
We will see this being used every day for the next 4 years, Islam calling out like the mythical Sirens of Sinbads voyage.