Brian Leiter asks an interesting question about the literature on religious toleration:
I'm wondering ... whether there are ... articles that try to argue why religion in particular should be tolerated, arguments that make claims appealing to distinctive features of religious belief and practices. Or as [Timothy] Macklem frames the question: "What is it that distinguished religious beliefs from other beliefs, so as to make them worthy of distinctive, perhaps superior constitutional protection"?
In other words, he's interested in arguments for tolerating religion qua religion which don't proceed from more general notions of autonomy or human flourishing. I think Leiter is right to say that "while religious toleration is often a paradigm case for discussions of toleration, the arguments for it are not specific to religion". The standard (liberal) case for religious toleration and religious freedom maintains that religious liberty is important for the same reason that individual liberty is important: we promote religious liberty in order that people be free to live autonomously and choose their own values.
I'm not sure, however, that an argument for according religion "superior constitutional protection", as Macklem puts it, would be an argument for toleration. There are lots of arguments out for there for according religion special protection - arguments from the tendency of religion to cultivate civic virtue, for example, which hold that religious beliefs ought to be considered worthy of respect in virtue of their content, rather than, as is the case in the liberal account, insofar as they are taken up freely. But could such arguments plausibly be construed as arguments for tolerating religion qua religion?