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The History of Religious Freedom in the U.S.

First Principles on the Right to Religious Freedom in the U.S.
The is the second in my two-part series on recent religious freedom laws.  The first covered the more practical considerations of how to think about the laws.  This entry is about first principles:  What is the history of religious freedom in the U.S., and what are our rights?

Overview
The 1st Amendment to the U.S. Constitution makes us consider religion as something special, trying to keep it free from entanglement with the government.  The government can neither help nor hurt religion.  What that means has been debatable, but in general everyone has long agreed that it definitely applies to complete liberty of belief and complete exclusion of a national religion.  Neutral laws that happen to affect religious observation, such as drug laws, have generally been held to be okay, but the laws cannot be aimed specifically at religion, except that Congress and the states can carefully craft exceptions for religious exemptions (such as conscientious objectors).  The "generally applicable" standard, stated most forcefully by Justice Scalia in 1993, is still the constitutional interpretation, but Congress can (and has) make general exemptions in federal law and specific exemptions in certain areas of state law.
 
Until the 20th century, there were very few enforceable individual religious liberty rights.  The Founding Fathers didn't much care about universal rights of any sort, and the states were free to have their own state religions.  Only after the "activist" US Supreme Court used the 14th Amendment to apply the 1st Amendment to the states did individual religious liberty become a legal reality.  In the mid-1960's we began to have some of these rights applied to businesses, too, not just the federal and state governments:  no discrimination on religion in areas like education, employment, and housing.
 
What is the 1st Amendment?
"Believing with you that religion is a matter which lies solely between Man & his God, that he owes account to none other for his faith or his worship, that the legitimate powers of government reach actions only, & not opinions, I contemplate with sovereign reverence that act of the whole American people which declared that their legislature should 'make no law respecting an establishment of religion, or prohibiting the free exercise thereof,' thus building a wall of separation between Church and State."  Thomas Jefferson in his letter to the Danbury Baptist Association, 1802.
The hypocritical purveyor of quotes for every occasion, Jefferson, drafted the memorable phrase about separation of church and state, so it was worth including here.
 
The wall of separation is there to protect against both sides:  Power-hungry clergy from taking control of state power (Establishment Clause) and power-hungry politicians from taking control of religious power (Free Exercise Clause).
 
Establishment Clause
  • The state cannot sponsor a religion.  There can be no Church of America, the federal government cannot provide a subsidy to the Baptist Church, the Catholic Church cannot represent us at the U.N., etc.
  • There can be no state religion, no religious requirement for office or employment, no religious expressions while state agents speak for the state.  This includes everyone from the President to a school teacher in Washington, DC.
  • What isn't prohibited: State people acting as individuals (in fact, these activities are protected); treating religious organizations like other organizations.
Free Exercise Clause
  • There can be no thought crime -- you can believe what you want.
  • There can be no singling out of a religious group -- something cannot be illegal BECAUSE it is religious.  If it is legal to butcher a pig for bacon, it is legal to do it for a religious ceremony.
  • What isn't prohibited: generally applicable laws that incidentally make religious exercise more difficult (no alcohol, no peyote, no animal cruelty, etc.).
Original Understanding
To show part of the original understanding of the government, see the Treaty of Tripoli, written under the Washington Administration and signed by President Adams, which declares that "The government of the United States is not, in any sense, founded on the Christian religion."  There is no official sanctioning of Christianity, and there is no official condemnation of Islam.  Or, for that matter, atheism or Satanism.
 
Application of the 1st Amendment
The 1st Amendment was originally aspirational and of small scope.  The right to religious freedom only applied at the national level until the 20th century (and even then, not so much).  The Founding Fathers didn't care too much about your religious freedom -- they just wanted control to reside at the state level, and it was completely okay that many states had state religions.  Remember, the Founding Fathers didn't care much about personal freedom, anyway ... unless you were rich white men with good connections.
 
The Civil War spawned the 14th Amendment, which eventually applied religious freedom mandates on the states.  The 1st Amendment itself was not applied to the states until halfway through the 20th century -- well after prohibition and women's suffrage, for instance.  Jehovah's Witnesses were at the Supreme Court from the late 30's through the 50's, fighting for the application of the Free Exercise Clause (and usually winning).  Until then, there was practically no legal freedom of religion.
 
Beyond the 1st Amendment 
The main expansion of religious liberty has been extremely controversial because there are competing religious expressions at stake:  Civil Rights laws.  Starting in 1964, laws began being passed that say businesses cannot exclude on religious belief in employment, education, credit, housing, and access to public facilities or public accommodations.
 
Most people focused on the race portion of these laws, but lately the cases have been about religion, like the Hobby Lobby case.  Does Congress have the power to pass laws that infringe on the liberty of businesses?  Is it proper for a government to intervene in areas of personal contract?  Does it matter if there is a great power disparity?  My first post covered a lot of this ground, so I won't belabor it again here, except to say that there is very little support in history to say Congress could not.
 
Religiously Motivated Additions to the Law
The 20th Century also had some movement in the other direction.  Eisenhower added "In God We Trust" to paper money (it had been on coins for some time, though) and "One Nation Under God" to the Pledge of Allegiance.  The are both obviously small establishments.
 
There have also been several attempts to put the 10 Commandments in public places like schools and courthouses.  There has been an interesting dichotomy in many of the arguments, though -- most public figures advocating such inclusion are explicitly doing so for religious reasons (Christianity is the key to morality, and the 10 Commandments are a succinct form of the morality), but often the lawyers arguing say the Commandments are actually historical artifacts and secular ... kinda like the Magna Carta. 
 
As a few of the Justices have noted, though ... no, they are not secular ("I am the LORD thy GOD" is secular?).  We can ignore it if we agree it has no religious meaning (but then who cares?), or we can say it is what the majority of Americans think (Christians, Jews, and Muslims).  Or we can just spit in everyone's face, if we happen to be from Alabama.

Legal tests and approaches
Establishment Clause: The Lemon Test (Lemon v. Kurtzman, 1971) has been eroded but still remains an important part of interpretation.  It says that, for the government not to run afoul of the Establishment Clause, there should be no excessive government entanglement, the government must not advance or inhibit religious practice, and any law must have a secular legislative purpose.
 
Free Exercise Clause: There have been several cases and laws on this, going different directions, but here is a breakdown of most of the modern important ones.
  • Free exercise covers opinions, not practices (Reynolds v. U.S., 1878) -- the first Free Exercise Clause case, holding that the Clause extended to opinions only, not action
  • Religion clauses apply to the states (Cantwell v. Connecticut, 1940, and Everson v. Board of Education, 1947) -- The 14th Amendment made religious freedom a fundamental right that the states could not abridge without due process
  • Sherbert Test (Sherbert v. Verner, 1963) -- strict scrutiny (the government must have a compelling government interest for its law and use the least restrictive means available to meet that interest), sometimes called "strict in theory, fatal in fact" because it is rare that the government can meet this really high standard.
  • Smith (Employment Division v. Smith, 1990) -- rational basis (the government must have some reason that is not illegitimate) for generally applicable laws, which generally means the government will win unless the law is pretty crazy
  • RFRA (Religious Freedom Restoration Act, 1993) -- strict scrutiny should apply to all laws substantially burdening individuals' free expressions of religion, even if generally applicable
  • Boerne (City of Boerne v. Flores, 1997) -- Congress can't make states/localities use strict scrutiny, and it can't dictate what the Constitution means ... but Congress can still use remedial means for federal law via the 14th Amendment
  • RLUIPA (Religious Land Use and Institutionalized Person Act, 2000) -- Partially in response to Boerne, Congress gave very targeted exemptions: Strict scrutiny for land use laws as applied to religious organizations, and strict scrutiny as applied to prisoners
  • Corporations are people, too (Hobby Lobby, 2014) -- Closely held private companies are "persons" for 1st Amendment purposes, and they therefore have religious freedom.
Conclusion
Freedom of religion has never been about freedom for evangelical Christians to have access to the powers of the government to enforce a theocratic view of the law -- it was designed in part to keep that from happening.  The notion, stated by several prominent conservatives such as Mike Huckabee, that Christians are "under attack" is patently ludicrous, but I do believe that some of the "Evangelical Christianity is special" aspects of our legal system have seen some defeats, and that is understandably scary to those who have drawn power by combining religion and politics (such as the former Baptist preacher and Arkansas governor Huckabee).  The spirit of the 1st Amendment, even back when it was only a small aspiration of slave holders, has always been to keep religion from getting power from the government and to keep government from getting power from religion.
 
The general pathway of tolerance has been starting with small aspirations toward liberty, and then slowly, over centuries' time, removing the ability for the powerful to impose their beliefs on the weak.  This started with the federal government, and then moved to state and local governments, and then moved to businesses engaging in public commerce.
 
The problem with making religious exceptions from neutral laws is that you have to define all sorts of things (what a religion is, how important a belief is, how sincerely the belief is held, etc.) to craft nuanced exemptions, and you quickly run into thought crime issues.  As a Quaker, I can refuse to go to war, but as a philosopher, I cannot.  Neutral laws are both more philosophically consistent and, in my opinion, more consistent with the spirit of the idea of a wall of separation.  That wall of separation is a good thing for religion and for the state.
 
Thoughts?

NOTE:  This post has been edited to explain some of the judicial standards above.

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