I would like to suggest that you read the Jan. 25 installment (scroll down a bit to get to it) of a correspondence that has been playing out between Andrew Sullivan's and Sam Harris on Sullivan's blog. Harris is the author of "The End of Faith" and "Letters to a Christian Nation." Sullivan makes a good case that they both agree that there may be a higher truth beyond our current understanding of empirical inquiry or proof.
That's why Sullivan says of Harris: "That's why you've gone on retreats, explored Buddhism, experimented with psilocybin, as I have." and then, "...that brings me to the asymmetry of our positions. We both accept that there may well be a higher truth beyond empirical inquiry or proof. I respect your opinions in this matter, and feel informed by them. You regard my opinions as inadmissible in public debate... you are being intolerant." (Sullivan writes in the context of the Christian canon and uses the "God" word with ease.)
But Sullivan actually gives Harris' (I think legitimate) reason for this intolerance earlier in his text: "You argue further that even if you concede the possibility of a legitimate form of religious truth-seeking, the content of various, competing revelations renders them dangerous. They are dangerous because they logically contradict each other. And since their claims are the most profound that we can imagine, human beings will often be compelled to fight for them."
The issue seems to me a practical one. there may be higher levels of universal truth, but conventional religions haven't proven a very effective way of revealing them in a form that can be agreed to by all of us humans that share a common evolutionary biology. Only rational empiricism has done that.