I'm no huge fan of O'Reilly's (that has been proven time and time again), but I'm not sure that I'm seeing the comparison that many in the gay community are making.
I will grant you that he is such a smug, smarmy guy that his joke about 'inviting al Qaeda next' came off really badly. But, I think that in the end it was just that, a joke. I would argue that anytime you want to make a funny, you probably shouldn't go after an entire segment of the population. But hey, it's his show, not mine (yet).