What's so special about religion that it needs special protection either in law or in ethics? How is it that some people are allowed to make stupid, crazy, or repugnant claims that are immune from criticism merely because they preface it with 'I believe' or 'God says'? Does no-one else find this state of affairs ridiculous? Here I want to focus on 3 mythical foundations for religion's special exemption: that religion is 1) individual; 2) ethical not metaphysical; and 3) concerned with beauty rather than truth.
1. Religion is not individual.
Enlightenment thinkers talked up the value and power of individual freedom of conscience so far that they seem to have persuaded themselves and their current liberal inheritors that the possibility of individual conscience is the same as its ubiquity. Historically, we can see how this understanding evolved from the core protestant doctrine of individual salvation through faith (not the church) and the modus vivendi that ended the 30 years war in Europe with the 1648 Treaty of Westphalia (restricting states' rights over individual faith).
But people do not do religion by themselves. (When they try, they usually end up sounding even loopier - 'we are not alone', 'my grandma's out there looking down at me', etc). It is a communal activity in which religious dogma and reasoning are passed on to others, especially children, and the faith of each is supported and confirmed by other community members. But this immediately contradicts the principle of individual conscience, which would seem to require that everyone's freedom from religion should be secured first, so that they can make up their own minds freely as adults in the full possession of their rational capacities. Consider the child who comes into school with a note from his parents "Little Johnny can't attend sex-ed classes because his religion forbids such awful things and he has a right to his beliefs based on his individual conscience". Just whose individual conscience is operative here?
2. Religion is metaphysical not ethical.
Religion is often said to be an ethically understood 'way of life', but in fact most religion is committed to a whole set of factual claims about the origins, nature, and working of the world. For example, God made man and woman and they fell from his favour; homosexuals are unnatural; supernatural forces and spirits constantly intervene in the world; etc. But if these are claims about worldly facts then they can be criticised as such and even disproved (e.g. with evidence of evolution, homosexual behaviour in other species, etc). This is important because many flawed ethical claims of religions stem directly or indirectly from an outdated or flawed metaphysics (a point often missed by ethicists!) Religious ethical principles are often directly and indirectly dependent on particular understandings of how the world works (e.g. religious opposition to abortion is surely concerned as much with a metaphysical belief that life begins at conception as with the direct religious instruction that 'life is sacred'; modern science suggests life is more incremental than on-off).
A religious metaphysics may be quite self-serving in supporting anachronistic social arrangements (women's restricted 'traditional' roles; isolating one's children from the godless and their inconveniently different opinions; etc) which is another reason they seek protection from the criticisms of science or common sense. A closed circle can be constructed in which the divine nature of the world justifies specific religious practises and social arrangements as part of the divine order, and that religious understanding of the world is itself justified by those practises. First gender roles are required by God's law. Then, when people ask why men and women are so different, the nature of the divine order is cited as the best explanation.
A bad metaphysics can have direct consequences for practical reasoning, for example if you see political problems in the middle-east in biblical terms or try to pray your dying child well. It can also affect the quality of politics since people who genuinely believe in a world very different from the one the rest of us live in will i) have radically different concerns and reasoning (bring on the 'End of Days!'), and ii) be more-or-less isolated from the normalising force of deep interaction with non-believers, marginalising themselves but also weakening the possibilities for a grown-up politics for the rest of us.
3. Religion is about truth not beauty.
Generous minded liberals often say that every individual has a human right to religion because every individual is engaged in a search for meaning that they must pursue in their own way as their conscience demands. That seems based on the 19th Century romantic combination of individual rationality and authenticity in which each individual in some sense creates their own unique interpretation of the meaningfulness of the universe. That certainly sounds lovely - religion then resembles an aesthetic pursuit pursued by individual artists (presumably related to other arts such as literature or painting). Religion therefore needs special protection to protect and respect these acts of creation. But of course, most people are not religious in that romantic way. They want the truth, and the right, not beauty, and they are conformists not artists. Religion is nowadays mostly practised moralistically and scientistically, not as a matter of subtle and intellectual aesthetic creativity.
The nature of religious belief has changed radically over time. Belief in, which resembled far more a personal commitment to the divine has been replaced by belief that, in which the content of beliefs becomes increasingly important and is asserted in a scientistic way. This phenomenon is not unconnected with the rise of protestantism (its schismatic creeds) and the pluralism following the reformation, but also with Enlightenment themes of empiricism and rationality which have driven religious groups to assert the literal truth of their previously rather mythologically understood sacred texts, in order to hold their own against the new paradigm of science. In the 19th century scientists came along and divided the world into empirical facts and nonsense, and religions responded by saying "we have facts too!" Not only do they end up looking ridiculous when they try to claim knowledge about the world based on religion, but they end up distorting the genuine humanistic resources of religious texts by reinterpreting them as a rigid dogma and embracing an impoverished theology restricted to narrow and shallow methods of reading and thought. It's a primitivist worldview in need of engaged criticism, not condescension, from the rest of us.
Liberalism requires respect for individuals and therefore toleration of what they choose to do. But that does not mean we have a duty to respect the ludicrous and harmful things many people say they believe in just because they say they are important to them! I'm not challenging the right of religious people to be religious and believe in fairies. But rather their claim to intellectual immunity - that the rest of us should keep a straight face while they rant. There is a clear epistemic duty in liberalism to support principles and institutions which help individuals base their beliefs and ethics on truth. Protecting religious institutions from scrutiny is a betrayal of that duty that can have bad consequences for individuals and liberalism itself. Of course not all religion is like this - mystical forms tend to eschew specific claims about the world, deeply theological forms in properly organised religions are at least capable of entering sensible debate - but those don't require protection from criticism to flourish. Such religion would actually benefit from a freer market of ideas that would strip away the veil of intellectual credibility from their more crackpot competitors.