(Cross-posted to prosblogion.)
Sceptical scenarios are usually taken to raise "A how do we know that not p?" question. But let's ignore that question. Of course, we are not brains in vats, there is no evil demon deceiving us about everything, most of our perceptual states have causes, and the world is more than five minutes old. The question how we know, or at least are justified in believing in, these facts is for the epistemologists to scratch their heads over, but we metaphysicians and natural theologians can take them for granted just as dentists and archaeologists do.
Nonetheless, there are genuinely metaphysical questions in the vicinity. Given a sceptical scenario p, we can ask: "Why is it not the case that p?" Why do we have bodies rather than just being brains, why are there no evil demons deceiving us about everything, why do at least most of our perceptual states have causes, and why did the world come into existence in inchoate form with a big bang, rather than fully-formed the way it was five minutes ago?
We can also ask the more general question: Why are all sceptical scenarios non-actual?
A theist has a fairly easy answer to the general question (essentially Descartes' answer): God is unlikely to permit persons to be generally deceived in ways that they cannot reasonably get out of no matter how hard they try. And this answer also works for the specific questions. An anti-realist has a way of getting out of the question by arguing that no distinction can be sensibly made between p and not-p.
The realist non-theist's best bet is to try to answer the specific questions one-by-one, because the prospects for a single answer to them all are poor. Thus, maybe, there are no evil demons because materialism is true. Our perceptual states have causes because a Causal Principle holds, either necessarily or contingently, and perhaps restricted in some way (I don't know that there is any good way to restrict it in a way that gives causes to most of our perceptual states but does not ground a cosmological argument, but that's a different debate). It's harder to explain why there are so few brains in a vat. Maybe one can talk about how brain-in-a-vat scenarios are unlikely to arise apart from certain kinds of agency (people vatting other people), and how these kinds of agency are not so likely to be exercised on a vast scale (or maybe that civilizations are likely to die out before they achieve the technology to turn people into brains in a vat), so that, most likely, most people are not brains in a vat.
The five minute hypothesis presents its special difficulties. Because the entropy of the universe five minutes ago is higher than the initial entropy of the universe, there is an intuitive argument that if the universe came into existence by chance, it is more likely to have come into existence much as it was five minutes ago than much as it was at the Big Bang. That's a tough one. Evolutionary theorists of mind can argue, however, that consciousness requires an evolutionary history, and hence it is impossible for minded beings to arise in accord with the five minute hypothesis. That probably won't help much with the fifty million or at least one billion year hypotheses. Or one might find some good physical reason why universes need to start in a lower entropy state than the that obtained five minutes ago. But it's a hard problem.
Can something like this be said for every sceptical scenario? Maybe, and maybe not. But notice that for a lot of these scenarios, what we will have said is something probabilistic. And unless the probabilities of non-actuality that these considerations yield for the individual scenarios are extremely high, that still leaves the question why no sceptical scenario (to do this argument in earnest, we'd need to explain this notion somewhat!) is actual. And whatever the probabilities are, the theist has a unified explanation of the apparent coincidence that for no sceptical scenario p, is it the case that p is true.