"Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof" The reach of this provision hinges on the word "law" - namely that it limits this sections applicability to official legislation, not to behavior by government officials that occurs in the absence of governmental sanction (which by the very nature of this statute is prohibited anyway).

However, the trick to understanding this amendment is to look beyond the words themselves. HOLD UP! THAT MEANS I'M ADVOCATING AN ACTIVIST VIEW OF THE CONSTITUTION! No, it doesn't. Legal interpretation of any law, not just this one, does not occur in a vacuum. It always includes a review of any official documentation that surrounded the law's derivation. Today we look to Congressional records from committees and such. In contemplating late 19th Century legislation, we must look to official papers published by those involved in a law's passing. The argument for/against that practice is moot. Suffice to say it is a practice that predates the existence of our country, has been practiced since its inception, and therefore is legally considered part of Common Law, contrary to what Antonin Scallia and Clarence Thomas would have us believe.

Thomas Jefferson wrote the most prolifically about this topic and summed up his views regarding a 1779 religious freedom law in Virginia thus:

"[N]o man shall be compelled to frequent or support any religious worship, place, or ministry whatsoever, nor shall be enforced, restrained, molested, or burthened in his body or goods, nor shall otherwise suffer, on account of his religious opinions or belief; but that all men shall be free to profess, and by argument to maintain, their opinions in matters of religion, and that the same shall in no wise diminish, enlarge, or affect their civil capacities."

It's safe to say that his views did not magically alter between that time and when the Bill of Rights were drawn up less than a decade later so we can accept this statement as applying to what he thought regarding this part of the 1st Amendment. Notice there is no mention of a "law" or "legislation" from a government but rather the idea of a person being "burthened" [burdened] or to "suffer" based on their existing beliefs by the government. The final part of that quote was written to address a recently repealed law that prevented Catholics from holding office but can logically be interpreted to apply to any activity a person may do on behalf of government.

Neither of those points is absolute - a person has a right not to be put upon religiously by a government just the same as a person holding office is not prevented from exercising religious freedoms. That equally means that a person holding office must not exercise his religious freedoms past the point where others not of his beliefs are forced to endure his religious ideology or practice. This means that Mr/Mrs Elected Person can profess all day long what they believe but in an office where they hold sway over another citizen (e.g. every government office and by extension every employee of that office) they cannot exercise their religion in an official capacity IF said citizen is made to feel burdoned or made to suffer because of those actions. Here, citizen means the entire general public.

It is further the burden of government and its officials not to take actions it knows violates this tenant. So even in the absence of a person saying, "Hey! I feel religiously put upon by this government action!", the government has the responsibility to not take actions it reasonably knows would cause such prohibited burden in the first place.

Bringing the article full circle then, while the 1st Amendment specifically addresses only a law, it is not restricted to that language but instead applies to all government action. It therefore holds that the freedoms favor the citizen over the government official and any actions he takes when acting on behalf of government (passing laws, displaying plaques, reciting prayer) in any official capacity but said official does not relinquish his own religious freedoms outside of his office.

The main issue on governmental action regarding religion is brought by those who confuse morality with religious practice. (Most of) The contents of the 10 Commandments are very admirable and the advocacy of their practice is a laudable goal, however a government office/official cannot display them in a government office because they are quite literally religious text. Nope, sorry - a person's office space or government grounds is still owned by the public at large. There is only cultural habit, not legal allowance, that a public official can make his office space a representative part of his life/personality. Likewise, there is no allowance for teaching religious viewpoints in public school (except as a purely academic pursuit such as for comparative religion or religious history study) since public schools are extensions of government.

As far as the recent brouhaha over the contraception mandate, there is no constitutional right to own a business or to even hold a job (don't confuse the Declaration of Independence with the Constitution). A church is allowed to run a university, adoption program, food kitchen etc. for no other reason than because the government does not prohibit it. The government is very much within its scope of powers to put restrictions/requirements on these organizations' activities with no allowance made for the religious beliefs of those that work there. This applies to extraneous organizations that fall outside the providence of church operations and not to intrinsic actions that are part of direct execution of religious activities.

The notion that companies have rights is not something I am going to address here and in the face of any precedent beyond Citizens United's free speech issue, I stand by what I just said.

Please notice that at no time did I reference the separation of church and state. I think that phrase is simplified sound bite taken from a speech Jefferson gave nearly 20 years after the Bill of Rights was passed.