Religion tends to be treated liberally where people who believe in the tenets of one religion exercise no power over people who believe differently.
Let's say you are a Rastafarian and for you, smoking marijuana is a sacred activity. Are you free to do so in the United States?
Let's say fundamentalist Islam gains strength in America and becomes a majority. Would the US tolerate a politics defined by seventh century ideas of morality expressed through a secular vehicle such as the US Congress?
Why is fundamentalist Christianity any different, when it seeks to impose its values on the US by secular means? For instance, by eroding the values of observed science in text books. Or by imputing its morality of "life" upon individuals whose beliefs differ.
Let me put it another way. The desire for freedom of religion is a rebuttable presumption and depends to an extent on circumstances. There are other principles which compete with religious freedom and virtuous outcomes are achieved only when these other principles are also considered.
For instance, the secular notion of a separation between church and state is generally honoured by US citizens as a whole as having a higher authority than the stipulations of any religious text. A US religion is not free to reject that division.
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