I think we are missing a basic truth here --
Skepticism is a method for evaluating a particular and specific claim. It cannot be used to directly confirm or dismiss a belief system as a whole. Sure, there are certain belief systems which tend to naturally arise from skepticism, but that is not the same thing as suggesting that good skepticism can only lead to a particular conclusion. Once you start making the claim that "good skeptic" = "a certain type of belief" you are turning skepticism from a method into a dogma.
To put it another way, such attitudes tend to encourage people to just jump to certain conclusions rather than reevaluating the evidence after each instance. A good skeptic should always be open to having his conclusions changed with new evidence, but when you start jumping to a particular assumption (as in "skeptic by definition equal atheist") you shortcircuit that process.
The simple fact is that two people can look at the same evidence and still come to different conclusions. Skepticism has to acknowledge that by limiting its criticism to specific claims and evidence. It's skepticism to say "As far as the evidence I've seen goes prayer does not directly aid in the healing process", but you start offering personal belief once you get to "Therefore, there is no god."
For instance, there are a number of skeptics (here and elsewhere) that honestly belief that the clear and obvious deduction based on "evidence" is that Libertarianism is the only logical political choice. I and others, however, would strongly dispute that. Does that mean we aren't good skeptics or is it that believers in Libertarianism aren't "real" skeptics? See how once you start confusing method with conclusion you turn the whole movement into an ideological crusade of one sort or another?
There is also another consideration -- we have access to different sources of evidence, some that aren't available to others.
Let's say that I am out walking in the woods one day when an alien mothership comes down out of the sky and some strange creature comes out to say "hi." Turns out he (it) is a friendly fellow just looking for directions to Tau Ceti. I point out which way to go, he thanks me, and then takes off. Amazed at my experience I rush to tell my next door (human) neighbor.
But, guess what, my neighbor doesn't believe me. After all, I didn't bring my camera and the alien didn't leave me his intergalatic business card. I have no independent evidence to back up my claim. Thus, from a skeptical viewpoint my experience is pretty much worthless -- it can't be used to establish the general conclusion that aliens exist and visit Earth. Yet, for me I have all the evidence required -- I was there and saw the alien first hand.
This sort of effect is quite common when it comes to religion/spirituality. People often have intensely meaningful, but also completely personal religious experiences. In fact, such things might ultimately represent that individual's reason for believing. But, obviously, such things can't be shared in the way that scientific facts can be -- that is, it is a subjective (as in individual) not objective (open to anyone) experience. We can all read a book on physics, but only Bob experiences his own unique religious revelation.
Now, that doesn't mean that such personal experience trumps all objective knowledge, only that it too is in the mix. We can't automatically dismiss such a thing just because we personally haven't had such an experience. By claiming that skepticism always leads to certain belief systems that is exactly what you are doing. It smacks of arrogance and others are going to pick up on it.
That's why I say skepticism is only a method for investigating claims, not a set of dogmas that any "good" skeptic should believe in.
