Darwin was not an atheist.
Why would a loving God keep his creation in the dark about their origin till thousands of years after Genesis was written?
Because explaining the TOE to a people barely out of the stone age would be a waste of time. You try and explain to people in Afghanistan today how a computer works and see how much success you have.
I figure, God gave us a rough sketch as to how the world began, then he moved on to explaining more important stuff, such as moral codes. He knew we would eventually reach a level where we could fill in the details of Genesis.