In discussing compatibility of science with religion, it's easy for atheists to miss the real problem with most religious beliefs. It's not that they conflict with science, it's that they conflict with critical reasoning.
For instance, if we're talking about moral beliefs based on some sacred text, there's obviously no scientific study that can show that they're incorrect. But critical thinking can show that this is a very poor basis for moral beliefs, as evidenced by all the other moral lessons from sacred texts that we do not accept.
And since critical thinking is advocated by skepticism, we should ask whether skepticism and religion are compatible.
I was going to divide "compatibility" into different definitions again, but then I decided that it was somewhat pointless.
If I said that science and religion are compatible or incompatible, then I'm talking about a particular set of methods and conclusions conflicting with religion. But critical thinking is much more broad than science. It's not just a set of methods to discern truth, it's the set of all methods which can discern truth. So if I just say that religion conflicts with critical thinking, I'm being awfully unspecific. All I've said is that there exists some line of reasoning which says religion is wrong. Which line of reasoning, you ask? One of the valid lines of reasoning.
To be fair, I might be using rather broad definitions of skepticism and critical thinking. Daniel Loxton recently stated his opinion that "the core claims of most religions are out of scope for science, and thus for scientific skepticism." This is based on his opinion that skepticism is properly narrow in scope, and goes no further than science. Thus, for Daniel Loxton, asking whether skepticism is compatible with religion is the same as asking whether science is compatible with religion.
Just as Daniel equated skepticism with science, I have equated skepticism with critical thinking. Maybe it really occupies a middle ground between science and critical thinking.
Skepticism can be a tricky thing to define. Luckily, the definition is moot; the classification of something as "skeptical" confers it no special authority.
We can ask the more practical question of how skeptical organizations and writers should treat the topic of religion. Incidentally, I am both a skeptical writer and a president of a skeptical organization. I have probably already expressed my opinions on the matter through my actions. But allow me to also express them through words.
The scope of skeptical discussion depends entirely on the context and medium. In a group of college students, there is little point in trying to cut off discussion of topics, just because they're not "skeptical" topics in the narrow sense. In a more formal context, like the Skeptical Inquirer, I hope the writers stay closer to science, at least on the magazine pages.
But whether the context is more formal or more relaxed, there is no point to enforcing conformity of religious beliefs. In fact, I would recommend against enforcing any sort of conformity at all, especially considering the individualism among skeptics.
If you're going to define skepticism as broadly as I have, there will be a lot of disagreement among skeptics on skeptical topics. I know several religious skeptical people, and yes, I do disagree with them. But then I also disagree with the vice-president's views on how evolution impacts morality. I disagree with the secretary's view of animal rights. Even if we limit ourselves to religion, I have some disagreements with my friends about the right way to refute the cosmological and ontological arguments.
If we discouraged disagreement on religion, that would not only be bad in itself, but also discourage other disagreements, since people will be afraid of "stepping out of line".
Some skeptics think that religion is somehow a fundamentally different kind of disagreement. How so? How does that merit different treatment?