Should the government give special rights to religious believers and religious institutions which no atheist or secular institution can have access to? That's what the Congress did with the Religious Freedom Restoration Act. Far from restoring religious freedom, it created special rights and privileges based on religion, allowing religious institutions to ignore neutral civil laws. The Supreme Court struck down the RFRA in Boerne v. Flores, reinforcing the principle of equality for all.
Built in 1923, St. Peter Catholic Church can seat around 230 worshippers, too few for the growing parish, so the Archbishop of San Antonio gave permission for alterations to enlarge the building. A few months later, the Boerne City Council passed an ordinance authorizing the city's Historic Landmark Commission to create a preservation plan for proposed historic landmarks and districts. Under the ordinance, construction affecting historic landmarks or buildings in a historic district had to be pre-approved by the Commission.
When the Archbishop applied for a building permit to enlarge the church, his application was denied by City authorities who relied on the ordinance and the designation of a historic district (which, they argued, included the church). The Archbishop challenged this in court under the Religious Freedom Restoration Act of 1993 (RFRA).
Congress had passed RFRA in response to the Supreme Court's decision in Employment Division, Dept. of Human Resources of Oregon v. Smith, which upheld a state law of "general applicability" criminalizing peyote use. This decision eliminated the balancing test created by Sherbert v. Verner, which asked whether the law at issue substantially burdens a religious practice and, if so, whether the burden is justified by a compelling government interest.
The RFRA prohibited "[g]overnment" from "substantially burden[ing]" a person's exercise of religion even if the burden results from a rule of general applicability unless the government can demonstrate the burden "(1) is in furtherance of a compelling governmental interest; and (2) is the least restrictive means of furthering that . . . interest." Essentially, the RFRA reestablished the authority of the Sherbert Test even though the Court had already rejected using that test anymore.
The District Court concluded that by enacting RFRA Congress exceeded the scope of its enforcement power under the Fourteenth Amendment. The Fifth Circuit reversed, finding RFRA to be constitutional.
With Justice Kennedy writing the majority opinion, the Supreme Court ruled against the Archbishop and in favor of the city, finding that the Congress did indeed exceed its authority by passing the RFRA.
In imposing RFRA's requirements on governments and laws, Congress had relied on the Fourteenth Amendment, which guarantees that no State shall make or enforce any law depriving any person of "life, liberty, or property, without due process of law," or denying any person the "equal protection of the laws," and empowers Congress "to enforce" those guarantees by "appropriate legislation."
The Supreme Court decided that the RFRA was not a proper exercise of Congress' power because it contradicted principles necessary to maintain separation of powers and the federal state balance:
If Congress could define its own powers by altering the Fourteenth Amendment's meaning, no longer would the Constitution be "superior paramount law, unchangeable by ordinary means." It would be "on a level with ordinary legislative acts, and, like other acts, ...alterable when the legislature shall please to alter it." ...Under this approach, it is difficult to conceive of a principle that would limit congressional power.
According to the Court, the RFRA's most serious shortcoming lay in the fact that it was so out of proportion to a supposed remedial or preventive goal that it cannot be understood as responsive to, or designed to prevent, unconstitutional behavior. Instead, it created a substantial change in constitutional protections, proscribing state conduct that the Fourteenth Amendment itself did not prohibit. Its sweeping coverage ensured intrusion at every level of government, displacing laws and prohibiting official actions of almost every description and regardless of subject matter:
...RFRA's legislative record lacks examples of any instances of generally applicable laws passed because of religious bigotry in the past 40 years. Rather, the emphasis of the RFRA hearings was on laws like the one at issue that place incidental burdens on religion. It is difficult to maintain that such laws are based on animus or hostility to the burdened religious practices or that they indicate some widespread pattern of religious discrimination in this country.
Most interesting for atheists is Justice Stevens' concurring opinion, in which he states:
In my opinion, the Religious Freedom Restoration Act of 1993 (RFRA) is a "law respecting an establishment of religion" that violates the First Amendment to the Constitution.
If the historic landmark on the hill in Boerne happened to be a museum or an art gallery owned by an atheist, it would not be eligible for an exemption from the city ordinances that forbid an enlargement of the structure. Because the landmark is owned by the Catholic Church, it is claimed that RFRA gives its owner a federal statutory entitlement to an exemption from a generally applicable, neutral civil law. Whether the Church would actually prevail under the statute or not, the statute has provided the Church with a legal weapon that no atheist or agnostic can obtain. This governmental preference for religion, as opposed to irreligion, is forbidden by the First Amendment. (see: Wallace v. Jaffee) [emphasis added]
This Court Decision found that the Congress was not permitted to force courts to use legal tests which they did not wish to use — the courts have jurisdiction over the means by which they decide whether or not laws are constitutional. Justice Stevens' opinion affirms the principle that religion cannot be preferred over non-religion by the government without violating the separation between church and state.