Darwin changed with the times at a period in history where industrialism was beginning to revolutionize society, and science had completely changed its perspective. Along with Darwin's explorations, many discoveries were taking place, placing God in a second to none place in comparison to the early Victorian period and late Hanoverian period where God was the center, cause, and effect of all that lived.
Comparatively, Darwin began his life as a true God-centered Christian. As society, the sciences, literature, and the economy of Victorian England began to change, a shift of ideals began to permeate the once eccentrically religious land. With it, Darwin refrained from taking sides and went from Christian to Agnostic, in the hopes of exploring in depth the scientific base of faith, and without denying the existence of something else out there.
This is a very difficult question to answer quickly because Darwin's religious views were quite complex and changed a lot over time.
First of all, by his own accounts, he was never an athiest. He always thought it unlikely that the universe could have been created solely by chance. He, at least at times, thought it was possible that the rules he laid out for evolution could have been imposed by God.
However, Darwin was no longer Christian by the time he wrote his most famous books. He thought the morality of the New Testament was "beautiful" but no longer believed that the book itself was the word of God.
For more on this very complex subject, follow the links I've provided.