A term that I think is generally covered up among the skeptic community is “scientism.” It’s a legitimate thing, and I think it’s a problem that it has risen, without philosophical backing, to be so common among skeptics. Briefly, scientism is the idea that the scientific method can be applied to the process of discovering truth in all matters. To summarize the argument against scientism, there is no basis on which to claim that science is somehow universally reasonable as a methodology. In other words, just because science has been useful for a significant number of questions up until this point does not imply that science is useful as a gauge of truth in all pursuits.
Religious folks or those otherwise skeptical about skepticism, as it were, often accuse the modern skeptical movement (often those in the “New Atheist” camp) of scientism, and the skeptics have done precious little to defend themselves against that claim. In fact, it seems a large number of them (e.g. Lawrence Krauss, Richard Dawkins, Sam Harris) are quite happy to admit and, if I may use the term, flaunt their scientism. I cannot say how much of it is actual evidence, logic-based belief and how much of it is an emotional tie. However, my suspicion is that scientism is largely an emotional issue, or at the very least a blatant misunderstanding of metaphysics.
Many skeptics, those earlier mentioned especially, are immediate turned away when I mention the concept of metaphysics. As I said, these folks have a predisposition to believing that all things must be explained by science. If such is the case, then if something is inexplicable by science (such as much of the pursuit of metaphysics), they are happy to brush it aside as poppycock. I’m not going to necessarily say they are wrong here. If someone came up to me and started to explain to me that they are truly, honestly an Aristotelean, I would laugh, perhaps quite rudely. There are some ideas about metaphysics which blatantly do undermine or contradict science, and I will agree with the skeptics that such claims can be reasonably dismissed. However, to throw away the entire pursuit of metaphysics based only on the idea that if something is not based on science, then it is worthless (or at least nothing better than a wild guess) is entirely unfounded on reason.
If I may interject, this is where brilliant men and women like Richard Dawkins and Lawrence Krauss (my favorite punching bags) are all too entirely destructive. A person listening to them or reading their philosophical works (e.g. The God Delusion) in a critical, knowledgable fashion can recognize most of their arguments as fundamentally baseless. The concept of God is, at least to a sophisticated philosopher or theologian, not a scientific claim, as Richard Dawkins purports. It is not reasonable to believe that science – a field heretofore confined to the material universe – must be the field that discovers what happens outside the material universe (before the big bang, for instance), as Lawrence Krauss purports. These are just a few examples of how scientism is actually dangerous to the pursuit of truth.
My studies and my thinking lead me to be an empiricist. I believe in science, and I believe in reason as a foundational principle in how we can discover truth. If we have evidence, that evidence should be used in a reasonable fashion to construct a truth narrative that is consistent with the rest of our truth narratives. While I do not have the space to defend these principles, I think that as the foundations of Western philosophy and science in the modern era, these are principles on which most of us can agree. In order for us to make a blanket statement that science is the sole criterion for truth, we need an incredible, mind-shattering amount of evidence. In other words, in order to establish the process of science as the sole methodology for determining truth, we must prove (a) that everything can be explained scientifically and (b) that other methods of seeking truth are always unreliable. As a philosophically generous person and a pragmatist, I might accept scientism if we can prove a significant majority of cases that fit these criteria. Of course, we do not even have that.
Science is a highly useful tool for understanding truth, but it has not yet knocked reason off its pedestal. Science and reason are cohorts in the quest to figure out how this reality in which we exist works, but one cannot exist without the other. The application of philosophy and rationality is as closely tied with our knowledge of that reality as is science. We cannot have truth without both.