About the only mainstream film that we could think of with an integral atheist hero and message at its core is the dramatisation of the Scopes Monkey Trial, Inherit the Wind. Brilliant though this film is, and explicitly atheistic through the poin of view of its hero, it is more akin to a documentary - being a fairly careful recreation of the events of that landmark trial - than a true fictitious piece of cinematic myth.
Also, it's like fifty years old and no one alive has heard of, still less seen it.
Well, we should correct that right away. This is a brilliant film, great fun for any rationalist or retro movie fan. Also should be noted, Donna Anderson is a stone fox.