Simoun. The show takes place in a futuristic theocracy that's fighting losing a war to several other nations. They fight using "the chariots of the Gods," which are flying machines built from lost technology. Lots of themes about a religion being exploited by the military and the lost of (a country's) purity. The characters sometimes manipulate the main crew's status as respected priestess (sibyl) for soldiers.
In one of the episodes, they try to turn the war around by breaking a taboo and opening of the holy machines, only to discover there is nothing inside. One of the characters has a mental breakdown at the emptiness. They also discover the religion of another country is similar to theirs, and speculate that they are worshiping manifestations of the same deity. Later it's revealed that the modern world was born when two of the main characters went back in time to the aftermath of a cataclysmic war, and fell from the sky in their aircraft. They gave hope to the people, taught them how to fly the machines, and in time people came to worship those that flew the machines. The ending is that they lose the war, but two of the main characters decide to escape through time, so they will remain young and "just as we are" forever. Everyone else must change and die, but they'll know that somewhere their two friends are still alive, blinking in and out of various skies, like goddesses really.
It's not really Atheistic, but it is an interesting show that picks up around episode 13.