It seems like he’s just using a rhetorical flourish. From the article:

“During his White House years, William Jefferson Clinton — someone Judge Sonia Sotomayor might call a “white male” — was dubbed “America’s first black president” by a black admirer. Applying the standard of identity politics and pandering to a special interest that earned Mr. Clinton that distinction, Barack Hussein Obama would have to be considered America’s first Muslim president.

This is not to say, necessarily, that Mr. Obama actually is a Muslim any more than Mr. Clinton actually is black”

Though he throws doubt in there with the “necessarily,” and an inflammatory headline, to appeal to the fearful.