Not everything has been explained, nor will it ever be. The important thing is that we have not observed anything that seems to require supernatural intervention for its explanation. There are some today who cling to the remaining gaps in our understanding (such as our ignorance about the origin of life) as evidence for God. But as time passes and more and more of these gaps are filled in, their position gives an impression of people desperately holding on to outmoded opinions.
The problem for religious belief is not just that science has explained a lot of odds and ends about the world. There is a second source of tension: that these explanations have cast increasing doubt on the special role of man, as an actor created by God to play a starring part in a great cosmic drama of sin and salvation. We have had to accept that our home, the earth, is just another planet circling the sun; our sun is just one of a hundred billion stars in a galaxy that is just one of billions of visible galaxies; and it may be that the whole expanding cloud of galaxies is just a small part of a much larger multiverse, most of whose parts are utterly inhospitable to life. As Richard Feynman has said, "The theory that it's all arranged as a stage for God to watch man's struggle for good and evil seems inadequate."
Most important so far has been the discovery by Charles Darwin and Alfred Russel Wallace that humans arose from earlier animals through natural selection acting on random heritable variations, with no need for a divine plan to explain the advent of humanity. This discovery led some, including Darwin, to lose their faith. It's not surprising that of all the discoveries of science, this is the one that continues most to disturb religious conservatives. I can imagine how disturbed they will feel in the future, when at last scientists learn how to understand human behavior in terms of the chemistry and physics of the brain, and nothing is left that needs to be explained by our having an immaterial soul.
Taken from his article Without God.