In reality, Darwin’s loss of faith was, as he recognised, gradual and complex. The reasons were not new – suffering always has been and always will be most serious challenge to Christianity – but they were newly focused. Plenty of Darwin’s scientific contemporaries….. could accommodate their Christian beliefs with the new theory. Indeed, as historian James Moore has remarked “with but few exceptions the leading Christian thinkers in Great Britain and America came to terms quite readily with Darwinism and evolution.”
But Darwin, brought up on William Paley’s harmonious, self-satisfied vision of creation, could not.
From brief and good article from The Guardian.