Well, if Obama ever prays to God, then leads the nation charging blindly into a stupid, disasterous war
then I think you'd see his faith-based programs and initiatives get the very same skeptical treatment as Bush's.
And if Obama's religious followers ever tried to force narrow-minded, backwards religious views on the whole society, just like Bush's followers who would have loved to ban abortion everywhere, then you'd see the same treatment.
It's simple. People are less scared of Obama's religious belief, and that of his followers, because it's a lot less dangerous for America.