I think the unfortunate answer to this question is directly ‘trial and error’.
Much as it would be great to make some grandoise claim about validity or statistics, the bitter truth is that just about every option has been tried and ‘put up’ is the best idea.
Religious people have been around for a VERY long time, and successfully addressing the problem has basically always ended in some kind of tolerance people can all live with. The alternatives have been ruthlessly tried:
Genocide: Hitler, obviously. While fighting most of the world, Germany is busily allocating scarce resources to murdering millions; obviously this did crap all to help them win WW2. That said, a society that takes this kind of extremist behavior greatly wounds their society. A different example would be the early Christian Church, under the Roman Empire, which created a series of martyrdom and very failed to destroy the faith. Obviously a poor idea, but tried.
Enforced Conformity: If we can laugh at the Spanish Inquisition because of a Monty Python sketch, this belies a different but horrible arrangement. This is also the current strategy of China’s Communist Party in dealing with its Muslim Uighur minority. Spain has been ruled by dictatorships for most of its history and lagged behind much of more open minded Europe, lost its colonial empire and paid several prices for behavior.
Put them somewhere else: The Pale of Settlement, Ghettos. Arguably the Mormon Trail. There’s the obvious problem that there’s only so many ‘elses’ on planet Earth, and so putting religious minorities on the ocean floor, Antarctica or outer space isn’t even slightly feasible. This list also includes the original pilgrims, whose religious differences inside England would have long legacies in the founding of the USA.
In addition to creating a great deal of poverty and raising questions of loyalty, this risks escalating into worse ideas above. And these minorities can very easily become different groups on their own, seeking independence. After all, if treated badly by a host nation, what do they owe that host nation.
Economics: You can tax based on religion. This actually worked fairly effectively in the raise of various Muslim nations, where tax benefits for conversion worked well. Given the severity of the other actions above, it’s clear that many people would rather be taxed than exiled, tortured or slain. This method still works, indirectly, as people who don’t support churches don’t donate to churches.
So this has some legs. Should churches be taxed? Should religious followers be given special taxes?
Ultimately, bear in mind that whatever rules are baked into the system will be used against anyone, including their creators. So a nation that actively promotes secular behavior with narrowly defined taxes might be reasonable; this is not, however, a direct attempt to swing poverty as a weapon.
Acceptance Or we decide that this isn’t worth the trouble, that we can all get along. Yes, deranged wacktards are going to be there, and they may lose the culture war on the installment plan, but the track record of nations that decide to say SCREW IT and move on is strong.
Prussia, the guys who unified Germany, said SCREW IT to Catholic/Protestant conflicts that had, in the 30 years war, killed one in five Germans.
Though culture wars have obscured it, the United States has done well with a general SCREW IT to State Religions in allowing a diverse society.
So the answer to this question is:
Because rights are based on what the most annoying, most difficult people get at the worst times.
Because great nations have opted to SCREW IT and it worked well.
But most of all, because its easier than not.