To cast Darwin as an atheist revolutionary bent on toppling the authority of God, as creationists often do, is to miss the complexity in his own internal struggles over the role of God in the universe.
Darwin was, after all, christened in the Anglican Church and, after eschewing medical school, trained as a parson. When he married his cousin, Emma Wedgwood, he committed to sharing his life and innermost thoughts with a devout Christian believer. It would turn out that his gradually ebbing faith would be a source of disagreement between them.
There was a fundamental conflict between the prevailing religious view that living things were specially designed by God, and Darwin's conviction that even the most complex developments, like the human eye in all its intricacy, could have, and did, arise through natural selection. Believers in design argued that since such sophisticated structures could not have come into being by chance, they must have been created by intelligence, and thus they proved the existence of God. But the mountain of evidence that Darwin accumulated over the years persuaded him that natural selection was sufficient to shape life, without Divine intervention.
The death of his daughter Annie in 1851 at age 10 proved a severe challenge to Darwin's faith; he could not ascribe such tragedies to the will of a Christian God. Eventually, he called himself an agnostic.
Thus, even though Darwin had sympathy with a religious view of life, he struggled to reconcile both his theory and the reality of human suffering with the theology of his day.