Skeptics and Believers
Why someone cannot be skeptical of certain claims of religion without necessarily being in one of the camps is beyond me. When analyzing a 'concept' such as a particular religion, (and it is important to look at particular religions because they cannot be lumped together), why does one need to provide a better alternative? One should be able to analyze it on it's own merit. That's like having a mathematical proof be overturned because the man who proved it turned out to be gay.
Next, about Science - the scientific method, with hypotheses and tests and controls and statistics, had only been practiced for at most a couple of hundred years. Prior to this time, there were what I would call pre-scientific discoveries in the areas of chemistry, physics, biology, upon which modern science rests. Furthermore, the symbiotic relationship between science and mathematics, as well as these disciplines and computational devices has only been established in the last fifty years. Already the rate of progress is astonishing. I am not predicting anything sensational, but if I were to compare religious thought and scientific thought, (as appley and orangey as they are) I would say that let the scientists have their 2000 years and let's see what they discover.
Finally, about Reason. Reason is abstract. It is a formalization of thought. Furthermore it is a refinement of thought. And lastly it is a gradient, not a scalar. What I mean by this, is that reasoning is not unique to humans. To some extent, many higher mammals reason - i.e. they are conscious of the world around them, of themselves, and they use facts about the world to be able to predict behaviors, and to use this to their benefit. In this way they are creating a mental model of reality. Man, due to whatever circumstances has been able to advance this to another level, due to perhaps language, perhaps genetic variation in the size of the cerebrum - really not important what specifically.
What is important to realize is that it is OK to not always be bound by Reason. Man, in general behaves reasonably, but He is not Mr. Spock or a computer. And that is OK. However, showing a counterexample where a person does something that doesn't follow Reason doesn't disprove the utility of Reason. It is not an all-or-nothing proposition!