York's passive-aggressive Jew-baiting elisions aside, my understanding of the whole "Felix" thing was that it was well-known that Allen detests his middle name. Allen's own rather peculiar family history came out because of Allen's own snide bullshit and a supposedly invented silly-name -- which I suppose is just what you want from a sitting U.S. Senator, someone who makes up silly names for hecklers -- and it all just cemented the derisive usage of Felix.
Allen greased his career by catering to the toxic underbelly of southern neo-confederate "culture". He pretended to be one of them, even though he grew up an O.C. rich-boy punk, he utilized all their totems and affectations, and he went to their little get-togethers. He knew exactly what he was doing, and he knew exactly what sort of people he was rolling with. That his revealed heritage (and his clear discomfort with it) might have bitten him in the ass once his buddies at the Council of Concerned Crackers found out he was a Red Sea pedestrian -- well, that's just sweeter than the dew on Scarlett Johansson's pooter.
As for Obama's middle name, who gives a shit? Maureen Dowd? Again, who gives a shit? Having said that, and seeing York's wink-is-as-good-as-a-nod-to-an-ignorant-cracker-douchebag æsthetic deployed, I'm sure we'll be hearing more of this sort of thing as Obama becomes the viable alternative to Hillary!-fatigue. It's called laying the groundwork, and the people who needed to hear it probably heard it just fine.