Religious Freedom Restoration Act's as a pure concept should not be that controversial.
No, really.
As a concept they should be very simple acts, "If the government imposes a rule or law that restricts or infringes on the religious beliefs of a person, the government must show a compelling government interest against a substantial burden for the rule or law."
Basically the government should not be able to interfere in the beliefs of a person with out a good reason and the standard of what a good reason is will be set at a very high level.
Example: a government imposes a dress code for school children that requires males to have hair that is shorter than their collars. A Sikh is attending and is told "cut your hair or don't come to school" (basically). The government would have to show that the hair rule is critical to the operation or safety of government activities. Not just making everyone be the same under the standards.
But a group trying to revive the Aztec religion with human sacrifice, the government would be able to show a compelling reason to interfere.
This should be pretty clear under the 1st amendment, but the past history of government vs religious belief has shown a need for making this clear. Which is why the pure concept only applies to the government and its interactions with religion.
This weird Indiana RFRA though applies to private businesses and exempting them from the laws is nuts.