Freedom of religion was one of the Founders' best ideas.
Our Founding Fathers weren't saints, but some of them were visionaries.
In the 18th century, much of Europe was run by state churches. Nations restricted political power to members of the right faith. Rival faiths and dissenting sects were persecuted, banned or both. Several of the American colonies had an established state church, and supported it with tax dollars.
The drafters of the Constitution could have written something along those lines, but they didn't. By the standards of the time, the document was radically irreligious. It began by declaring that the people of America, not God, established the nation. It opened federal office to everyone, regardless of their religious beliefs. The First Amendment banned Congress from establishing a church or interfering with Americans' right to worship as they chose.
As George Washington put it in his letter to a Jewish congregation in Newport, RI, 'all possess alike liberty of conscience and immunities of citizenship. It is now no more that toleration is spoken of as if it were the indulgence of one class of people that another enjoyed the exercise of their inherent natural rights.' Unlike so much of the world, the United States would offer 'to bigotry no sanction, to persecution no assistance.'
Two hundred and thirty-eight years later, that's still a radical idea. In much of world, religious access to power is seen as a matter of life and death. Hindus and Muslims lock horns in India. Saudi Arabia and Iran are repressive theocracies. China and North Korea both impose harsh controls on religion.
Even here, there are plenty of people who think their church/sect/religion should run the country. At the very least their faith should be able to impose its morality on nonbelievers, or exclude other faiths from exercising their "inherent natural rights." Washington was an optimist: toleration of other faiths is the most many of us can manage. And sometimes not even that.
Still, toleration is way better than I see some parts of the world achieve. And the Constitution and the courts do put brakes on the theocratic impulse to force other people to live and worship the "right" way. The sheer number of creeds, sects, religions and churches (not to mention the unchurched, the secular and the complete unbelievers) that flourish in an atmosphere of religious freedom helps reinforce it. Everyone's got a stake in not letting someone else become a theocrat. A fair number of people are willing to stand up for someone else's religious freedom, even when their own isn't at risk.
This is a positive thing. Much as I loathe religious authoritarians, we'd be much worse off if the law allowed the government or anyone else to silence theocrats, or silence anyone of any faith (keeping in mind that telling someone they're full of shit is not silencing them). Religious freedom isn't just a rule, it's a positive good.
Admittedly all this freedom makes life in America complicated. There's lots of disagreement on the line between religious rights and religion imposing on someone else's rights. Religious disputes factor into everything from abortion to gay rights to prayer in schools. Frequently when government treats religions (and no religion) equally, someone involved feels oppressed because their faith didn't win the fight. Sometimes government does in fact cross the line and restrict religious freedom too much.
In a theocracy it would be simpler, smoother, easier. The official religion wins every time, everyone else loses. Absolute power can be very efficient.
But the First Amendment isn't about efficiency or freedom from conflict, it's about justice. It's about those inherent natural rights of which Washington spoke. The freedom to worship one God, fifty gods or no god, as we choose, regardless of whether our neighbors like it. We are a long way from truly giving to bigotry no sanction, but the ideal remains alive. Some day, maybe we'll achieve it. Until then, we'll keep arguing.
To paraphrase Churchill, freedom of religion is the worst possible system. Except for all the others.