We are all natural-born theologians. What is it but faith seeking understanding that children express with their sequences of "Why?"
The faith that question expresses -- particularly when asked iteratively of the answers it receive -- is that there is a reason that something is the way it is. More than that, this reason -- or logos, if we're feeling fancy -- not only exists but is knowable by human intellect.
There's an irony in the fact that, these days, many of the people most devoted to asking why have convinced themselves that it is not a theological question. People who base their entire world-view on the ability of the human intellect to answer the question "Why?" lose their nerve and start doubting -- some even loudly denounce -- their one true method just when the reason gets interesting.
Those without religious faith who say they trust science don't trust science. They may trust physics, or cosmology (though often enough they really just trust certain physicists and cosmologists). But what we call the Scientific Method -- which by construction limits the circumstances under which you may ask why -- could more accurately be called the Engineering Trick. It's a formalized way of bounding the answer you're obliged (or permitted) to provide. This bounding does two helpful things: it keeps you focused on providing answers that might be of some more-or-less practical use to someone; and it lets you actually provide an answer in this lifetime. The unbounded "Why?", as any three-year-old knows, has an unbounded answer.
Now, unbounded logos is that which we call God (and some of us have learned to call unbounded logos, qua logos the Son of God). Bounded logos is that which we call science. (That's probably too glib, but close enough for rhetorical purposes, I think.)
The process of asking why again and again to each successive answer can end in one of three ways: admission of ignorance; voluntarism; or mystery.
Admission of ignorance is perfectly acceptable, and really the only acceptable answer from someone who really is ignorant. This, I'd say, is where properly conducted modern science winds up. We know the causes surrounding the object of study, and if these causes themselves depend on further, unknown causes -- if, to put it starkly, we don't really know the reason -- we can still make use of the relationships we do know about.
The parent who says, "Because I said so!" or the cosmologist who says, "Because that's what Planck's Constant is in this universe," is making a declaration of voluntarism, that fundamentally there is no intelligible reason something is the way it is. Even this can be an acceptable answer, especially at bedtime. But neither the natural scientist nor the theologian ought to wind up as a voluntarist.
"Because God says so!" is voluntarism when it's meant as the final, complete answer to why something is the way it is. Since, however, God has revealed something of His mind -- and, more importantly, something of His heart -- to us, we should never accept that (or really any other statement) as the final, complete answer. Granted that may suffice for purposes of moral reasoning, the understanding of faith leads always into the unbounded mystery of the Holy Trinity.
To the question, "Why?" we might always answer, "I don't know exactly, but I'm working on it."