According to the Will Wright (who identifies himself as an atheist in the interview).
Apparently, some people were upset that religion was included at all in the game. It doesn't say just what exactly those are or how religion is supposed to work in Spore, so it's anybody's guess just what the fuss is over. Given the game is rated E, it's doubtful that's it's anything particularly offensive - probably just a totem for your critters to dance around as a way of a getting a social edge on other tribes. That hardly seems like something anybody should really get worked up over.
In fact, I rather like the inclusion of religion in video games. In Civilization 4, religion is entirely benign - shoring up culture and happiness levels, and all religions give exactly the same bonuses. In Rise of Nations, you can upgrade your temple from religion to monotheism to existentialism, which I think is hilarious, since the implication is that as the society advances, it moves away from religion into something more philosophical. In Medieval 2 Total War, you see more of a darker side of religion, with crusading (or jihading) armies let loose on one's enemy, as well as priests, imams, and heretics converting populations. Heh, one of my favorite strategies after inevitably getting excommunicated was to personally lead my army's vengeance on the Papal states.
The interesting thing about religion in video games is that it's almost always religious people who are the ones who are easily offended, particularly RPGs that feature demons or warlocks. World of Warcraft is a prime example of a video game that some Christians feel uncomfortable about. I can't help but feel sorry for the zealots who become trapped by their irrational fears and miss out on a lot of popular culture as well as more moderate believers agonizing over whether or not a game is too ungodly to play.
I guess my main thrust here is not to take video games too seriously and get bent out of shape about religion being in it. After all, it's extremely common for religion to play some role in the civilization-crafting games. So, chillax, you alleged offended Spore-playing atheists and play nice or I'll sic my Spore FSM on your home planet. ^_^