First, I think we're all tolerant of religion and most other kinds of irrationality. There is a difference between tolerance and respect.
Second, there isn't much difference between beliefs that are contradicted by empirical evidence and beliefs that have no evidence for or against them, but are a priori very implausible. Both have a very low likelihood of being true and should therefore be considered false by rational people.
Third, I don't see how conceding that one's beliefs are irrational excuses the irrationality (unless we're talking about mind states that are beyond our control, like phobias). In most cases, such a concession is a symptom of a deeper, more insidious kind of irrationality. After all, what do theists mean when they say that their beliefs aren't rational, but they believe them anyway? Obviously they don't use the word 'rational' the way most of us do. Usually they mean that they know that their beliefs aren't supported by logic or evidence, but they believe there are 'other ways' of discovering truth, which is just smoke to hide the fact that they don't want to question their beliefs.
I would like to argue that there could be a more tolerant view of religion/theism here on Less Wrong. The extent to which theism is vilified here seems disproportionate to me.
It depends on the specific scenario how terrible religion is. It is easy to look at the very worst examples of religion and conclude that religion can be irrational in a terribly wrong way. However, religion can also be nearly rational. Considering that any way we view the world is an illusion to some extent. Indeed the whole point of this site is to learn ways to shed more of our illusions, not that we have no illusions.
There are the religious beliefs that contradict empirical observation and those that are independent of it...
A) Could it be rational for a person to hold beliefs that are independent of empirical observation if (a) the person concedes that they are
irrationalnot empirically based and (b) is willing to drop them if they prove to not be useful?B) Could it be rational for a person to hold unusual beliefs as a result of contradicting empirical observations?
As a least convenient world exercise, what is the most rational belief in God that you can think of?