To begin with, the First Amendment is flagrantly biased in favor of religion. As we all know, it requires Congress not to make any law “prohibiting the free exercise thereof.” What this means in practice is profound: If the beliefs you are exercising are not religious, your freedom to exercise them is not as protected by the Constitution as religious beliefs. If you like to trip on peyote because it is fun for you, or because you believe it makes you a better person, you will not receive the same legal protection as someone who trips on peyote because it is an integral part of long-standing religious beliefs to which they subscribe.
For irreligious people, this is a potential outrage of the first order. How dare the government extend special protections to religions for no better reason than that they are religions?
But for civil libertarians, whatever their degree of faith, there is cause for anxiety as well. The First Amendment implicitly requires government itself to make official determinations about what is and what isn’t a religion. No matter how necessary that may be to our constitutional framework, there is always a possibility for abuse, and in times of intense culture war, that possibility is magnified.
Unfortunately, the problem is even worse than that. The First Amendment is also biased against religion in an unexpected way.