Why Tolerate Religion?

Is there a "principled argument" why the "state should tolerate religion as such at all"?  Brian Leiter has posted a new paper, "Why Tolerate Religion?", on SSRN.    Here is the abstract:

Religious toleration has long been the paradigm of the liberal ideal of toleration of group differences, as reflected in both the constitutions of the major Western democracies and in the theoretical literature explaining and justifying these practices. While the historical reasons for the special “pride of place” accorded religious toleration are familiar, what is surprising is that no one has been able to articulate a credible principled argument for tolerating religion qua religion: that is, an argument that would explain why, as a matter of moral or other principle, we ought to accord special legal and moral treatment to religious practices. There are, to be sure, principled arguments for why the state ought to tolerate a plethora of private choices, commitments, and practices of its citizenry, but none of these single out religion for anything like the special treatment it is accorded in, for example, American and Canadian constitutional law. So why tolerate religion? Not because of anything that has to do with it being religion as such - or so this paper argues.

Professor Leiter's paper is provocative and engaging.  (In places, and somewhat to my surprise, it struck me as consonant with John Garvey's "Free Exercise and the Values of Religious Liberty.")  I think there is a lot to the claim (explored and developed by, for example, Steve Smith) that, at the end of the day, arguments for distinctive and special protection for religious freedom -- and, more generally, for the public authority's responsibility to promote and protect the common good, one aspect of which is religious freedom -- will (have to) be "religious" arguments (or, at least, not "liberal" arguments).