I grew up in the Bible Belt of the deep South in the 1950s. In addition to the Jim Crow racist regime white protestant Christianity dominated the whole society. The school day in public school began with a Bible reading and there were prayers at football games and band concerts. The law criminalized a wide range of sexual activity and abortion. If I had been living in California then, the established religious privilege would perhaps have been slightly less obvious, but the impact on people's private lives would have been the same. You could choose which denomination you wanted to belong to and some people were more ardent in their religious practices than others but almost nobody would refuse to at least give lip service to the appropriateness of religious observance. Traditional Christianity occupied a position of very strong social privilege.
A lot of things have changed since then. The social upheavals began in the 60s with the racial civil rights movement and the student movement that turned into the anti-war movement. The Warren court had already begun to turn over some traditional apple carts with liberal decisions in the 50s and their activities gathered steam. Second wave feminism and LGBT rights movements took their first root in the climate of ferment. Women's rights have made major progress on multiple fronts. Roe v Wade was an early victory for reproductive choice. LGBT rights have had a long slog, but they have also come a long way.
These and other social changes now pose a serious threat to the social conservatives who firmly believe that their religious views should still occupy the place of privilege that they did in the 1950s. They have been making consistent efforts to roll back the clock. Roe v Wade has been trimmed and constrained by later court decisions. Anti-abortion activist have found numerous means of restricting access to safe abortion services on a practical and political basis. The battles over marriage equality has brought all manner of resistance such as the infamous prop 8. These battles are a rear guard effort to continue the imposition of conservative religious beliefs on the rest of society. That seems to have become an increasingly minority position on a national basis. It still holds sway in the deep red states.
Conservatives have more recently launched what is to an extent a new front in their legal battles. They are making various attempts to establish a right for their beliefs as freedom of conscience under the terms of the protections provided by the first amendment. Freedom of conscience is an idea that goes back to the beginning of the enlightenment and it is definitely embodied in the notions that gave rise to the first amendment. The question posed in this context is what does "the free exercise of religion" mean in the 21st C. Most of us would likely associate that phrase with the ability of adherents of a particular religious persuasion to freely assemble and practice their forms of religious observance. It is now being asserted that laws and regulations should not compel individual or certain corporate persons to engage in activities which are contrary to their religious beliefs.
Marriage equality is one issue that has been a lightening rod for freedom of conscience. There have been several instances where service providers such as photographers, florists and caterers have refused to provide their services for gay or lesbian weddings. This is seen as being in a clash with their legal responsibilities under various public accommodation laws. It is also being asserted in conjunction with the mandate under the ACA to provide contraceptive health care without cost to the employee. That position has now been given support by the conservative majority on SCOTUS in the recent Hobby Lobby decision. This without doubt raises the probability that a variety of groups will seek to use that decision as a basis for claims for exemption form various laws and regulations.
We have long seen instances of first amendment rights being accorded to unpopular minorities. The ACLU came into wide spread disrepute when they successfully represented the American Nazi party. In Snyder v Phelps SCOTUS in an 8-1 decision held that the widely unpopular members of Westboro Baptist Church had a first amendment right to picket military funerals as an act of protest against gay rights. More recently in McCullen v Caokley the court found unanimously that the extent of the restrictions imposed on protesters at an abortion clinic unnecessarily burdened their first amendment rights. The legal concept of this combination of freedom of conscience and freedom of speech it not something new. In many instances it finds acceptance by both the liberal and conservatives on the court.
I personally find both of the decisions that I just referenced to be ethically distasteful to say the very least. But they are tied to a long standing legal tradition. The situation with the ACA is less familiar and settled ground. It is a sweeping new law that makes some major changes about the funding of health care and has been controversial in many respects. The issues about reproductive care have been a hot point of debate from the beginning. The Stumph amendment added at the last minute prohibited any requirements for providing coverage for abortions. The law also carried a built in exemption for churches which are nonprofit corporations, from being required to cover contraceptive care. Other religiously affiliated nonprofit corporations later objected to the requirement and the Obama administration extended the accommodation to them. Before Hobby Lobby got to SCOTUS, corporations were being given a right to religious accommodation and freedom of conscience. So the issue would seem to be how far such an accommodation should be extended not whether or not such a rights actually exists. In this case there was a very sharp division on the court between the conservative majority and the liberal minority. This is by no means a matter of settled law. What religious accommodation comes down to in practice is balancing such rights against compelling government policy responsibilities.
In essence what we have here is a very large segment of the population, religious conservatives, attempting to represent themselves as a minority whose civil rights are being abused by the majority. The battles over the past 50 years have been about women and minorities attempting to force concessions and accommodations from a conservative establishment. That process would now seem to be at something of a crossroads.