The Religious Freedom Restoration Act was passed in 1993 by a Democratic Congress and signed into law by President Clinton. The Supreme Court then struck down part of it, the part that applied to state and local actions, but upheld its application in federal law. In that case, City of Boerne v Flores, Justice John Paul Stevens wrote a concurrence that said this:
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.
This is exactly right. RFRA, and its companion law RLUIPA (Religious Land Use and Institutionalized Persons Act), give to religious individuals and organizations — and only religious individuals and organizations — the right to get out of laws that apply to everyone else. This is quite obviously a violation of the First Amendment and the Equal Protection Clause of the 14th Amendment.