Over on The Other board, they've got a "rewatching BSG" thread going too. And it is interesting, how atheists have a problem with the ending but theists find it deeply rewarding. The poser There can't figure out what the ending meant--even though by Season 1(?) Head Six was explaining that she was an angel from God. The problem is, if you don't believe in God, you skip the blatantly obvious cues. You wait for the payoff when Science explains why Laura and the cleric thought she was the dying leader that would lead the tribes to Earth. But if God is really behind it all...that is unpossible. Even when we blatantly see Starbuck die--and then come back, in an inexplicably mint Viper--and then find her own body on Earth...they're like "I can't wait to see how they explain that God isn't real."
Only they never do. Because in this story, God is real. Oh, maybe he's not a superhuman omnipotent old white dude with a beard and white robes. "He" may be some kind of alien we don't understand. But "He" is definitely real. And behind everything that has happened. And Godless people can't wrap their brains around that ending.