Stargate is the only one I can think of. They spend the entire series fighting gods, generally encouraging skepticism and confidence in naturalism in the peoples that they try to free while commonly telling people to not give in to arguments from their own incredulity.
On that note, The Lion King is secretly atheist--for one moment, where Timon says "You mean a bunch of royal dead guys are watching us?" in response to Simba's having put forward the story his father told him. Of course, the rest of the movie is kinda hypertraditionalist, but whatever.
Does anyone know about any other shows that could be called "atheistic" like this--that I can get on basic cable, mind you.