Conflicts continually arise between individuals and the government over religious freedom. For example:
Some religious groups teach that parents should not immunize children against childhood diseases. This conflicts with the state's interest in preserving public health. Other religious groups are opposed to decorations and ornaments; this can conflict with the state's requirement that slow-moving vehicles display lights and signs. A lumber interest might want to create a road through an area that Natives consider sacred. During the 1980's, the U.S. Supreme Court considered a number of such cases. A trend appeared in which the court appeared to give less importance to religious considerations.
In 1990, the Supreme Court issued a decision in the case of Employment Division vs. Smith. It involved the right of an native person to follow his religious tradition which involved smoking an hallucinogenic substance. The court established that governments could burden (restrict) religious freedom, as long as the law was neutral and applied to all persons equally. This decision prompted lower courts subsequently to allow additional government restrictions on religious freedom.
Dozens of groups concerned with religious freedom then joined together to form a Coalition for the Free Exercise of Religion. Their goal was to reverse this gradual erosion of basic religious freedoms in the United States. In an unprecedented show of unanimity, organizations representing very diverse belief systems joined forces. The list includes some interesting pairings of groups:
American Civil Liberties Union and the Traditional Values Coalition American Muslim Council and American Jewish Committee American Humanist Association and the Jesuit Social Ministries National Association of Evangelicals and the National Council of Churches Church of Jesus Christ of Latter-day Saints and the Unitarian Universalist Association and 56 other groups representing Christianity, Humanism, Islam, Judaism, Native American spirituality, Scientology, Secularism, Sikhism, Unitarian Universalism and various civil rights causes.
Partly as a result of pressure from the Coalition, the US Congress passed the Religious Freedom Restoration Act (RFRA) in late 1993. Overwhelming bipartisan support was shown. (Reference 42 U.S. Code 2000bb). Its key clauses are:
3 (a) In General: Government shall not substantially burden a person's exercise of religion even if the burden results from a rule of general applicability, except as provided in subsection (b). 3 (b) Exception: Government may substantially burden a person's exercise of religion only if it demonstrates that application of the burden to the person: 
(1) is in furtherance of a compelling governmental interest; and (2) is the least restrictive means of furthering that compelling governmental interest. 5 (1) the term 'government' includes a branch, department, agency, instrumentality, and official (or other person acting under color of law) of the United States, a State, or a subdivision of a State; 5 (2) the term 'State' includes the District of Columbia, the Commonwealth of Puerto Rico, and each territory and possession of the United States;
In summary: religious freedom shall not be limited except when a government can prove a "compelling interest" to do so. And then, the government must select a method that results in the least possible interference with religious freedoms of individuals, churches and other organizations. This is a very onerous burden on the government, and applies to every law that is passed.
This law had a major influence in over 90 court decisions since it was enacted late in 1993.
An interesting case (City of Boerne v. Flores, No. 95-2074) arose in 1996. It involved the Roman Catholic Archbishop of San Antonio, TX. The city of Boerne TX refused to issue a construction permit which would have allowed the church to expand into a historical district. The expansion was needed because of an increase in the size of the congregation. The church sued under the RFRA; the federal judge determined that the act was unconstitutional. It has since been reviewed by several appeals courts who have ruled the act constitutional. In mid October, 1996, the Supreme Court of the US agreed to rule on the case. They issued their ruling on 1997-JUN-25, declaring the law to be unconstitutional. The vote was 6 to 3.
Congress will now consider a new RFRA bill that might guarantee religious rights while staying within constitutional boundaries. Senator Edward Kennedy (D, MA), "We cannot take this 'no' from the Supreme Court as the final answer." In the meantime, several states have passed a law very similar to the original RFRA; these may well be unconstitutional.
From: ReligiousTolerance.org