Is Barack Obama a Muslim? Almost certainly not. Was he ever a Muslim? Almost certainly yes.
Barack Obama is "almost certainly" not a Muslim? No, he's not a Muslim, period. This isn't controversial.
Was he ever a Muslim? Again, no, he wasn't, unless we define it by birthright, in which case it switches from being utterly false to meaningless. Almost certainly, at no point did Barack Obama consciously identify as being Muslim (and if showing up in temple a few times is enough to make you part of a religion, anyone who ever grew up in Bethesda is Jewish through Bar Mitzvah ceremonies alone).