Atheist:

Science is made up of two components. First, there is a body of findings (observations and other data, provisional laws and other hypotheses, etc). Scientific findings are strictly about the natural realm. In this respect science will always be compatible with any religion that restricts its claims to the spiritual realm. (It may, however, contradict those religions that make claims about the world, as creationism does.)

Second, there is scientific methodology, which is ratiocinative rather than fideistic, empirical rather than aprioristic, fallibilist rather than dogmatic, collaborative rather than individualistic, public rather than esoteric, and -- heigh ho! -- it assumes that everything has a natural explanation/cause rather than a supernatural one. At the very foundations of science, then, on which everything rests, we find a practice that is antithetical to religion and an axiom that leaves no room for God.

Theist:

True, if Newton had believed that the motion of the moon depended on divine whim, he would not have bothered to find regular and universal laws of nature. But outside of his life as a physicist, he was a devout Christian. In general, a physicist may believe that physics can be explained naturally while believing that the existence of life cannot; a biologist may believe that life can be explained naturally while believing that the human mind, or the human spirit, cannot; a psychologist may believe that the psyche can be explained naturally while believing that the motions of the heavens cannot. You can be a scientist, and hence a naturalist, in limited domains.

Atheist:

Agreed -- if you choose to allow the scientific attitude in just select domains, you can consistently adopt a religious attitude in others. All I'm saying is: if you choose to adopt the scientific attitude generally, then you cannot consistently be a theist; you cannot hold any of the following.

If you have reason to give up the hypothesis that every phenomenon has a natural explanation, you should have an idea as to which domains lie beyond scientific understanding. And if you believe that it is futile to study certain domains, you should oppose taxpayer funding of certain sciences. (Granted, many religionists do oppose taxpayer funding of certain kinds of research, but they do so on moral grounds. For instance, they oppose experiments on cloning because they hold cloning to be wrong, not because they hold such experiments as a waste of money that's sure to go nowhere.)

By no means are you obliged to accept the principle that we should at least try to understand all known phenomena scientifically. But if you do accept such scientism, you should know that that may commit you to either agnosticism or positive atheism.