Much of the conflict of ideas relating to religion in America can be depicted as a conflict of epistemologies, namely, of an inductive approach to truth versus a deductive approach. Call it science versus religion. Call it natural versus revealed revelation. Call it open-mindedness versus presuppositionalism. Call it rationalism versus empiricism. Call it "philosophy" versus "theology."
The one approach starts with certain assumptions and proceeds to integrate experience with those assumptions. The other starts with experience and builds general conclusions from there. Of course Kant pointed out that we inevitably use both. We have certain "innate" frameworks through which we filter experience (cause-effect, for example).
So what may seem like obvious choices turn out to be rather muddy in reality. Yes, we all process reality by way of certain presuppositions. But how big should these be? Some presuppositionalists see these as huge macro-systems where if you accept one thing as a presupposition, you must then accept the entire system. This is nothing but lunacy that blows away like a puff of smoke against the smallest stepping out of doors.
Then again, some empiricists pretend like they are completely objective and have no intrinsic biases or starting points. Once again, this is lunacy that evaporates on the smallest peak of light.
In a perfect world, these two would coincide precisely--the general conclusions to which our experiences build would coincide with the general presuppositions from which we start. In life, of course, these often conflict. We get out of our birth zone and find other personalities and other cultures out there. Those who come out of the cave recognize that some of their assumptions were options rather than absolutes and that some of their assumptions were just wrong.
Since presuppositions are only subject to revision--they are assumptions rather than evidentiary in nature, they can be tricky. There is a tendency for various epistemological tribes to treat them as unfalsifiable. This of course means that those who do not share the same assumptions cannot really have a conversation with them. Those who have the assumptions are, in a sense, the "elect" and that is that.
However, at some point the common sense "tests" for truth may become overwhelming. Presuppositions may come into conflict with experience. Presuppositions may shout of incoherence. Presuppositions may fail to "work" in life. For most there will be a breaking point, where epistemological stubbornness yields to a gush of reality.
Let me skip to the end. The two kingdoms of deduction and induction best work together. We need a core set of micro-assumptions to think at all. The micro-assumptions of deduction are logic. The micro-assumptions of induction are a generalized form of the scientific method.
The best epistemological model for the Christian is "faith seeking understanding." In my opinion, faith must in theory be falsifiable or else our claims to be a people of truth are meaningless. To pass muster as claims about truth, faith must be modifiable and subject to critique.
And we must also recognize that easy answers like the church or the Bible are not as easy as you might think on more detailed examination. For example, not only is the interpretation of the Bible subject to significant debate at countless points, but even when we feel relatively certain about its original meaning, we must then determine how God wants us to apply it today in varied contexts. Protestants by historic definition reject any absoluteness to the trajectory of the church.
This is not to say, however, that evidence is absolutely determinative. It can be coherent to have faith despite the appearance of the evidentiary landscape, because all data is subject to interpretation. In that case, however, one should be honest about the lay of the evidence and invoke some degree of blind faith. To be coherent, the invocation of blind faith may require one to modify basic common sense understandings of the world. Few of those who would invoke blind faith in this way can thus be consistent with the way they live the rest of their lives.
Some thoughts I've shared before...