That's the question asked by Irwin Tessman in the January/February 2008 issue of Skeptical Inquirer. Tessman is a Professor Emeritus in the Biology Department at Purdue University. You can see a podcast of his lecture, "A Darwinian View of a Hostile Atheist" at [The Society of Non-Theists at Purdue University].
Tessman is interested in comparing the views of the so-called "militant atheist," Richard Dawkins with the religious views of Charles Darwin. He concludes that their views are not very different. The biggest difference between the two men is that Darwin choose to hide his lack of religion from the public in deference to his wife Emma, who was a devout Anglican.
With the publication of the compete text of Darwin's autobiography in 1958, we now have much greater insight into Darwin's thoughts about religion. Here's how Tessman puts it,
Where does Darwin stand on the matter of a personal God? "The old argument of design in nature, as given by Paley, which seemed so conclusive, fails now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by a man" (Darwin 1958, p.87). Darwin seems to reject the idea of a personal God and, therefore, theism too. His religious views are difficult to pin down (Browne, 2006, p.46), but something close to deism would seem to fit.There seems to be general agreement that Darwin did not subscribe to the tenets of any organized religion. There is debate over whether he believed in supernatural beings. His Grandfather, father, and brother were non-believers so it's reasonable to suppose that Darwin was too.
Theism is a belief in a personal God, one who responds to prayers and interferes in daily events; atheism is the opposite of theism. Deism is the belief in a God who set the universe in motion whit all the physical laws and both sacred and learned commentaries, but was absent after that. In practice, deism is much like atheism.
He may have been comfortable with agnostic, a term that was invented by his friend Thomas Huxley. This would have been far more acceptable to Emma than atheist. I suspect that if Darwin were alive today he would be an atheist ... unless Emma were also alive.
Browne, Janet (2006) Darwin's Origin of Species: A biography. Douglas & McIntyre Vancouver/Toronto.
Darwin, Charles (1958) The Autobiography of Charles Darwin, Nora Barlow ed. W.W. Norton and Company, New York.