When we stake out a position on a particular issue, we would like to believe that we are drawn to it by the logic that supports the side on which we come down. This is seldom the case, and not simply because humans can be led against reason by emotion. Instead, it is because the positions we take stem from the values we hold. This sounds tautological, but an example should illustrate what I mean.
Recent debates about gun control aren't really about gun control. No appeal to statistics is likely to move minds because people are really arguing about something else. Nor do the sides even really disagree about the final end: a reduction in violence is sought by all. Disagreement concerns the means by which this end will be acheived. So one side believes government can be trusted to regulate firearms, while the other puts its trust in a well-armed populace.
These positions are ultimately derived from first principles, but, more importantly, within a tradition that tries to examine the ramifications of such principles.
As the philosopher Alasdair MacIntyre points out in his excellent book, Whose Justice? Which Rationality?:
It is a Cartesian error, fostered by a misunderstanding of Euclidean geometry, to suppose that first by an initial act of apprehension we can comprehend the full meaning of the premises of a deductive system and then only secondly proceed to enquire what follows from them. In fact it is only insofar as we understand what follows from those premises that we understand the premises themselves. If and as we begin from the premises, our initial apprehension will characteristically be partial and incomplete, increasing as we understand what it is that these premises do and do not entail. pp. 174-5
With this in mind, let's switch topics; instead of gun control, we're going to focus on the existence of God. These discussions tend to be pretty fruitless; with MacIntrye's insight, we can see why this is the case. After defining his terms, a well-informed theist might pull out his Summa and begin to cover Aquinas's fivefold proof for God's existence. This isn't a terrible way to go about it, but it tends to fall short as the rejoinder to a discussion of an unmoved mover is: "Who moved God?" It's not a ridiculous question, but it is rather unhelpful, in that we're thrust back upon the definitions of terms.
The genius of the Summa is not the fivefold proof, but the systematic way in which St. Thomas builds his system. We shouldn't cede ground to the agnostics and atheists and admit that Thomas's proofs are mere formalities, quick jots to move us along to meatier matters. And yet, if we pretend that this is the case, how many other things become apparent? We can't get to God's simplicity if we don't get past His existence, just as we can't get to the Secundae Partis until we finish the Prima Pars; for one part of his masterpiece depends on another, and Thomas is nothing if not thorough. His thought must be evaluated as a whole, which might not require that one read the entirety of the Summa, but it does require that one do more than reject his proofs and move on to something else.
Back to God's existence. If Thomas--and others; I am a dedicated if hopelessly amateur Thomist, but there are other theistic systems of thought, most notably that of St. Augustine--if theistic philosophers have examined the ramifications of there positions, it's far from clear that atheists and agnostics have done the same. Certainly there were philosophers who tried to do so, most famously Kant, who was not an agnostic, but philosophized like one. He rejected tradition in favor of an attempt to concoct a moral system derived from unaided reason. Yet Kant, for all his brilliance, failed, as MacIntyre pointed out:
In moral philosophy the central question which the participants in those debates had hoped to answer was: What are those principles governing action to which no rational human being can deny his or her assent? Hume's appeal to rational consensus concerning the passions, Kant's formulations of the categorical imperative and the principle of utility were all attempts to supply an answer to this question. Yet each one of these answers turned out to be susceptible of rejection by the adherents of rival answers, whose claims to rational justification were as much and as little contestable as those of its opponents. p. 176
Even more frustrating than the cavalier dismissal of theism is the arrogance of many modern atheists. Richard Dawkins is their pope, but he seems just as oblivious to the failure of the Enlightenment. Granted, they do not like what the Church has to say about sex--and here at least Freud may have a point; it is usually about sex--God must not exist. But they have not explains how we shall be moral--or what being moral will entail. It is unlikely that Dawkins will succeed where Kant failed; in fact, as MacIntrye makes clear, it's impossible. But they seem to have simply glanced over this dilemma, blithely confident that we can just take the good parts of an ethical code without all that awful shame over mild indiscretions. Unfortunately for them, that's not how traditions work.