I am wondering whether any readers know of literature making the case for toleration of religion qua religion. What has struck me in reading the literature is that while religious toleration is often a paradigm case for discussions of toleration, the arguments for it are not specific to religion: arguments from autonomy and well-being would equally well encompass toleration of many other kinds of belief that are not religious in character; the Lockean argument is not specific to religion, since state tools for coercion are ineffective in inculcating belief simpliciter, not simply religious belief; Millian arguments from versions of the Harm Principle cast the net much more widely than religion; and so on.
The only exception to this generalization I have found in the literature is an interesting paper by Timothy Macklem (Law, King's College, London) on "Faith as a Secular Value," which appeared in the McGill Law Journal in February 2000. Macklem argues that the distinctive religious state, faith, is one that has a special value that warrants its special treatment in liberal societies. I don't think the argument succeeds, but that's not what concerns me here. What I'm wondering is whether there are other 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 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?" That, to my mind, would be an argument for religious toleration.
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