Many Christians and Muslims, and to a lesser extent Jews, think that Darwinian evolution requires or implies atheism, a charge first brought when Darwin was still alive. The Princeton theologian Charles Hodge argued this in his What is Darwinism? (1874). But Darwin himself, and many of his followers such as Kingsley, Asa Gray, and his friend Rev. John Innes, an Anglican local minister, thought not. Darwin, however, did lose his religious beliefs, ending up a self-confessed agnostic.
Partly the problem here lies in the term “Darwinism”. While some, like Alfred Russel Wallace, the “co-discoverer” of natural selection, used the term to refer to the general ideas of Darwin on evolution, others, such as the German naturalist Ernst Haeckel, used it to refer to a melange of philosophical, theological and political views, and it came to be seen as an ideology that was anti-religion. Haeckel himself was very opposed to Catholicism, and his “Monism” was a mixture of Enlightenment ideas, anti-clericalism and evolution. But he had a theology in which God was identical to the universe, and in which consciousness was innate.
Since the famous Scopes Monkey Trial in 1925 in Tennessee, it has become common to think that evolutionary biology is atheistic. However, as Dobzhansky and others such as modern biologist Francisco Ayala, demonstrate, many theists accept the reality of evolution. What they object to, if they do, is “Darwinism”. Since this is largely undefined, each author giving their own interpretation based on what they think is implied by evolution (both those who think it is atheism and this is a good thing, and those who think it is atheism and this is a bad thing), we do not need to think the biology requires atheism. The reason for this is that claims about the existence of God or gods are a philosophical problem. Just as the physics of the big bang neither confirm nor deny the existence of deities, neither do any other facts about the world. Any theology that is realistic must deal with the world as it is, not as theology would want it to be.
Some theologies are not realistic. For example, to assert that the world was created around 6000 years ago requires not only the rejection of biology, but geology, chemistry, physics, astronomy and in general reason. Likewise any theology that says the world is older than science tells us, for example some Hindu theologies, are equally unrealistic. To assert these doctrines, a theology must deny that science even works. In short, they have to deny that facts are facts. Butler would be appalled. So too would Henry Drummond, who in his reconciliation of theology and science, The Ascent of Man (1894) argued that one ought not find God in the Gaps:
There are reverent minds who ceaselessly scan the fields of Nature and the books of Science in search of gaps – gaps which they will fill up with God. As if God lived in gaps? What view of Nature or of Truth is theirs whose interest in Science is not in what it can explain but in what it cannot, whose quest is ignorance not knowledge, whose daily dread is that the cloud may lift, and who, as darkness melts from this field or from that, begin to tremble for the place of His abode? What needs altering in such finely jealous souls is at once their view of Nature and of God. Nature is God’s writing, and can only tell the truth; God is light, and in Him is no darkness at all. 
Finding God in the gaps of knowledge means that if those gaps are filled by science the room for God is decreased. If a believer wants a realistic faith, then they must deal with the world as it is. This means that some beliefs – that humanity is only explicable as the direct creation of God at one time, that the sun rises and sets because God makes it do so, or that life originated 6000 years ago – have to go. They are contrary to the facts.
It is a reasonable argument that in fact God of the gaps is itself a form of atheism. It implies that one can only believe in God if one disbelieves in the world, and since most (not all) religions do believe in the world, the only conclusion is that God does not exist. This is a view taken by critics of religion as well as creationists: believe that the world is older than (one interpretation of) the scriptures say, and the sole alternative is atheism. It is a black-and-white fallacy, or a false dichotomy. Disbelieve the world if you like (and be a Gnostic or Manichean), and then the problem does not arise, but if you believe the world exists as we know it, you have to deal with it in your theology. This is the modern problem facing religion, and not just with respect to evolution, but everything.
So Darwinian evolution presents no problem to religion that isn’t presented by all the other sciences. It is not a special problem for faith. Some religious thinkers will attack what they call scientism, the view that all that can be known must be known by science, or the promise of science. Most conciliatory theology, however, assumes that while matters of fact can be known only by science, theological truths are known by revelation or intuition or meditation. This no science can undercut, although a thinker who believes that if there is no evidence for a belief that belief is objectionable will make that inference. The believer, however, will not. I leave it to the reader to decide which way they wish to jump. It is, in the end, a philosophical decision, not a scientific one.
I have tried to work through the threads of the most common problems and issues that religion has historically had with evolution. While my preferred solution is that God is best seen as a primary cause, not a secondary cause, that is only one among many solutions offered by religious thinkers, and anyway I am not a believer, so the problem does not arise for me. However, I think that it is possible to deal with Darwin’s stone house and to believe in a providential God. The rest is up to you. As Darwin wrote shortly after the publication of The Origin to Asa Gray:
I feel most deeply that the whole subject is too profound for the human intellect. A dog might as well speculate on the mind of Newton. Let each man hope and believe what he can. Certainly I agree with you that my views are not at all necessarily atheistical. The lightning kills a man, whether a good one or bad one, owing to the excessively complex action of natural laws. A child (who may turn out an idiot) is born by the action of even more complex laws, and I can see no reason why a man, or other animals, may not have been aboriginally produced by other laws, and that all these laws may have been expressly designed by an omniscient Creator, who foresaw every future event and consequence. But the more I think the more bewildered I become… [May 22, 1860]
Let each person hope and believe what they can.