I really want to rewatch the whole series sometime, because I saw, I think, the first three and a half seasons and then didn't see the rest of season four until years later - and all of this was after it had stopped airing, so I wasn't in the middle of the contemporary discussion of it. Googling now, apparently the religious stuff was seen as a response to post-9/11 America, people perceived the Cylons as an Al-Qaeda analog, etc. etc...