See Alan Roebuck's "No Evidence for God?" in Intellectual Conservative for a useful treatment of the tendency of atheists to beg the question against theism by simply assuming, without basis, something like naturalism, materialism, or positivism to be true -- in other words, assuming the natural/material/empirically observable world is all there is.
While you're at it, check out one atheist's near-perfect instantiation of this tendency when he challenges theists to debate him... on a few conditions:
* By "knowledge and facts" I mean factual, scientific proof. No personal opinions, appeals to revelation, quoting the bible, no arguments purely from quoting an authority without actual evidence, personal/second-hand stories that cannot be confirmed, and no "philosophical bullshit.” **
** By "philosophical bullshit" I am referring to the fact that philosophy is not the most reliable method of getting at the truth. The sciences and empiricism are the most reliable methods of getting at the truth, not simple thought experiments, or philosophizing.
Of course, whether or not science is the fullest description of reality is precisely what is at issue here; taking it off the table simply begs the question against theism. And the claim that science alone is the basis of all knowledge is at once a philosophical assertion and a nonscientific one (as all epistemological claims necessarily are) -- and thus is simply self-refuting. The only way to get around this irreconcilable contradiction is to indulge in what Voegelin called the prohibition of questioning, a better example of which I couldn't have asked for.