In opening, I made two assertions that may need to be explained: that skepticism is not part of science and that skepticism is a philosophy of science. Both statements may be addressed by looking at the prominent schools of thought within the "community" of scientific philosophers. The majority of views can be placed in one of two schools of thought: Popperian or Kuhnian, so named after Sir Karl Popper and Thomas Kuhn.
Popper's view of the philosophy of science is essentially what most of us were taught in school, a more detailed version of the observation/hypothesis/experiment model. (Those of you saying to yourself, "It's science! What's so hard about that?" are probably Popperian.) The watermark of Popper's view is the emphasis on falsibility; that is, if it can't be tested, it's not science. Unique events are outside the realm of science; no theory is exempt from challenge irrespective of how well entrenched; and scientists test their theories. By contrast, Kuhn argued that science is what scientists do, and therefore science is a kind of consensus-seeking relativism. In fairness, Kuhn himself was not far removed from Popper, with Kuhn placing his emphasis on problem solving as the defining aspect of science. Unfortunately, his disciples took the philosophy farther and farther away from any absolute standard until the Kuhnian school was more focused on hierarchies, theorem-choice, and "problemshift." (I hate those phrases. Hierarchies are "who's on top of the pecking order," theorem-choice is "which theory will yield more profitable results" and problemshift is a made-up academic word that even the people who use it don't know what it means. As best I can explain it, problemshift is "I got this part figured out, but answering that question just created new questions." As knowledge on a subject is acquired, the emphasis of the research changes; think of it as "the problem is shifting.")
Lest I be guilty of oversimplifying, let me quote here from Imre Lakatos' paper, "Falsification and the Methodology of Scientific Research Programmes." (Book: Criticism and the Growth of Knowledge by Imre Lakatos and Alan Musgrave, New York: Cambridge University Press, 1970.)
Note: I have chosen to quote Lakatos rather than Popper and Kuhn directly for reasons of brevity. Lakatos does a very good job with the text of explaining the positions of both men and, on various points, criticizing and defending both. The few (ellipsis) edits I have made are also for space.
"…In his [Popper's] view, virtue lies not in caution in avoiding errors, but in ruthlessness in eliminating them. Boldness in conjectures on the one hand and austerity in refutations on the other: this is Popper's recipe. Intellectual honesty does not consist in trying to entrench, or establish one's position by proving (or 'probabilifying') it--intellectual honesty consists rather in specifying precisely the conditions under which one is willing to give up one's position…Belief may be a regrettably unavoidable biological weakness to be kept under the control of criticism: but commitment is for Popper an outright crime.
"Kuhn thinks otherwise…His main problem too is scientific revolution. But while according to Popper science is 'revolution in permanence', and criticism the heart of the scientific enterprise, according to Kuhn revolution is exceptional and, indeed, extra-scientific, and criticism is, in 'normal' times, anathema. Indeed for Kuhn the transition from criticism to commitment marks the point where progress--and 'normal' science--begins. For him the idea that on 'refutation' one can demand the rejection, the elimination of a theory, is 'naïve' falsificationism. Criticism of the dominant theory and proposals of new theories are only allowed in the rare moments of 'crisis'…
"For Popper scientific change is rational or a least rationally reconstructible and falls in the realm of the logic of discovery. For Kuhn scientific change--from one 'paradigm' to another--is a mystical conversion which is not and cannot be governed by rules of reason and which falls totally within the realm of the (social) psychology of discovery."
My primary purpose is not to debate the merits of the various philosophies of science. I am of the Popperian school and I think Sir Karl himself did a much better job of laying out his arguments than I ever could. Instead, I have provided the thumbnail sketch of Popper's and Kuhn's views to explain my earlier contentions: that (a) in the Popperian philosophy of science, skepticism is not part of science (data is data, there is no hierarchy of data or overwhelming burden of proof, just raw fact) and (b) that skepticism is a philosophy of science, specifically a descendant of the Kuhnian school of relativism complete with all of its built-in socio-political baggage. Once skepticism is understood as a philosophy, its flaws and dangers are much clearer, as is an understanding of its methods and the behavior of its proponents.
In short, the philosophy of skepticism establishes an orthodoxy within science. It places an unreasonable burden of proof on any theory or concept that would compete with what the orthodoxy has already accepted. It establishes this orthodoxy based on consensus (a social activity) rather than experimentation (a scientific activity). Finally, it sets up the skeptic as a kind of high priest and defender of the faith, rooting out the heretic under the mandate of fighting "irrationalism."
Please understand, I am not accusing everyone who considers himself a skeptic of holding these views or acting in this manner—many do not—but I do contend that these are the ultimate conclusions to be drawn from the skeptical school of thought. Moreover, in my opinion, this leaves skepticism in a position to do a considerable amount of harm, suppress large amounts of 'inconvenient' data, easily be abused by those with political ambitions who wish to hide under the banner of 'science as truth,' and in return contribute very little, if anything, to science or society itself. In addition, skepticism is a philosophy of reductionism, determinism, and materialism. Its logical conclusions have led us to theories such as that the conscious mind is epiphenomenal (that the idea that we have free will or are anything more than meat puppets is an illusion, and what we perceive as consciousness is just a side-effect of a mechanistic series of chemical reactions.) I've always wondered, if you really believe something like that, why are you bothering to try to convince me of it? Why talk to me at all?
At the Kuhnian-skeptical end of the road there is a relativism that says the mind is meat and man is an animal. At that point, there is no basis for either morality or ethics. I realize I may be accused of creating a straw-man version of it at this point and trying to tarnish the skeptical viewpoint by fear-mongering, but I don't think so. A philosophy should be tested by considering what its extreme version looks like because sooner or later, someone will go there. Of course, such a standard cannot be used to invalidate a philosophy (humans are humans and they will abuse anything if it serves their purposes) but, in weighing the merits of a philosophy, this extreme view should factor into the calculation. (The extreme application of Darwinian eugenics leads to genocide. It's been argued that extreme Christianity bombs abortion clinics, but a more honest view of the extreme end of the Christian philosophy are people like the Shakers. Agree or disagree, the very fact that we are discussing moral, social, and political repercussions simply reinforces that point.)
By contrast, I am also not implying that I believe aliens built the Egyptian pyramids right after Edgar Cayce traveled back in time to channel the wisdom of ancient Atlantis for them. But here I appeal less to the monolith of Science than to simple common sense. We are allowed to think for ourselves without having an official 'Science Guy Approved' sticker on our forehead. Likewise, science is not the only way of knowing truth or even things. As Sir Karl himself noted, just because something is not scientific, it does not follow that it is therefore not true or valuable. The proposition that science assumes to itself all that is true or of value is another side-effect of the Kuhnian school's dominance in academia. A tool is just a tool. Tools are meant to be used, not worshipped.