One of the founding myths of the United States is that religious liberty is enshrined because people fled to the colonies to escape religious persecution and the strong connections between the church and state in Europe. Whatever the truth of the matter, these are two excellent reasons to legally protect religious liberty. After all, persecuting people based on their faith (or lack thereof) seems to be generally wrong. Concentrating secular and theological power has often proven dangerous—although the church and the state can be quite harmful operating on their own (see, for example, Pol Pot or the scandals plaguing various churches). As such, freedom of religion seems generally a good thing—albeit within limits.
It might strike some as odd that religious liberty should be limited, but it is the nature of freedoms that they require limitations to exist. To say that freedom requires limiting freedom might seem paradoxical or Orwellian, but it is neither. Consider, for example, the freedom to own property. As Hobbes argued in his Leviathan, if everyone has the right to everything, then this amounts to a right to nothing. As Hobbes and others have noted, meaningful property rights require limiting property rights. To illustrate, for you to own your phone or house, it follows that my liberty to own or use them must be limited. The same applies to other freedoms and rights. For example, your right to life puts limits on the freedoms of others—they are not free to murder you. The same obviously applies to religious liberty—for you to have freedom of religion, others must be restricted in their ability to compel you to practice a different faith or to forbid you from practicing your faith. As such, to accept religious liberty in a meaningful sense is to accept that it has limits. The practical challenge is sorting out these limits—a matter of grave concern in the areas of religion, law and ethics.
One sensible approach to freedoms is to use that taken by John Stuart Mill. Mill argues that freedom should be set on utilitarian grounds using a principle of harm. The gist of his approach is that if what you are doing does not harm anyone else, then you should be free to act (or think) in that way. If your action harms others, then this provides a reason to limit your freedom. As would be expected, this approach is often applied to religious freedom. To illustrate, it would seem unreasonable to tolerate human sacrifice on the grounds of religious liberty. This can also be seen as an evaluation of which right trumps the other. In the case of human sacrifice, it can be argued that the right to life takes precedence over the right to practice one’s religion. As a practical matter, as Mill noted, people tend to take the view that what they like should be allowed and what they dislike should be forbidden—without any general principle in operation beyond liking and disliking.
Some would argue that religious freedom has been weaponized to be used against homosexuals and women. For example, there are those who argue that discrimination against homosexuals in housing, employment, medical matters and so on is justified by the religious views of those who claim that homosexuality is against their religion. In the case of women, there are those who contend that their religious liberty should allow them to refuse to provide contraception or abortion services to women. There are, of course, those who say that they are just defending true religious freedom—it just so happens that it seems to discriminate against homosexuals or women.
One interesting point is that if religious freedom allows such discrimination against homosexuals, then it would allow discrimination against anyone—provided that the person engaged in discrimination had the right sort of religion. For example, Christianity would seem to warrant discrimination against liars, adulterers, those who worship graven images, witches, those who misuse the name of God, those who do not respect their mother and father, and so on. Consistency would seem to require that if homosexuals can be discriminated against because their behavior is seen as violating sincerely held religious beliefs, then the same would apply to all sinners. That is all of us—for we are all guilty of some sin or another. Probably many. Oddly enough, there seems to be little interest in denying services to adulterers and liars (which is fortunate for a certain president) even though adultery and lying make it into the Ten Commandments and homosexuality is mentioned but once and apparently as being on par with eating shellfish. One might suspect that many proponents of this sort of religious freedom are really looking for a way to justify their discrimination rather than being overly concerned with acting consistently in accord with their professed faith. After all, if one should be allowed to discriminate against homosexuals because they are engaged in what one regards as sinful behaviors, then the same should apply to all sins. This, of course, seems absurd since it would warrant discrimination against everyone. So, let he is without sin engage in the first discrimination.