I have often thought, and I think some historians of science agree, that Darwin’s loss of faith was due more to the death of his daughter, than it was any certainty he put in some new found evidence, theory, or fact that was bound up in evolution—as far as God’s existence. This might lend some weight to the idea that some forms of agnosticism and atheism are emotional and psychological responses to events in one’s life and not some cold, logical, reasoned conclusion reached in a laboratory.
Knowing religion’s ubiquitous presence historically and world-wide, he did explore reasons for how it may have simply evolved naturally but he never posited any certainty here.
Also of note is the sense he had of what we might call the mystery and awe of existence. His response to seeing the rain forests for the first time was, “Silence hosanna”. Further, he wrote regarding such moments:
“Both [the beauty and cruelty of the world] are temples filled with the varied productions of the God of Nature: no one can stand in these solitudes unmoved, and not feel that there is more in man than the mere breath of his body.”
So Darwin was certainly a mixed bag. In this interview here, it is noted he had a “life-long interest in religion.” The death of his daughter may have caused him to lose faith in the traditional Anglican faith he had grown up in, but that is quite different from the suggestion by some that he ends up a faith-less atheist or philosophical naturalist. He was a naturalist in the sense of the word as it was understood at the time. It was not associated then like it is now with a hard-core sort of atheism/materialism.
From the interview:
“…I’d say that Darwin teaches us that it is quite natural for humans to be religious and that it is appropriate for Darwinians to be curious about why humans seek a religious purpose to their lives. That doesn’t require that we think that religion is entirely artificial. That it’s merely a coping mechanism. One can be a Darwinian without having to condemn religion or the sense—a sense that Darwin often explored—that there is something more.”
“I differ here from Richard Dawkins or Christopher Hitchens and other well known atheists, as well as probably a number of Darwin scholars, in that I’d say that Darwin has made it possible to be an intellectually fulfilled theist. As for Romanes, I believe he shows us that theology and faith can play a positive role in a Darwinian frame inasmuch our longing for eternity is more than a scientific question.”