Over the last few decades there have been two competing views of the deference owed to religious rights by the government. One has been a more restrictive view. Under this view, the government need not exercise any particular concern over whether any particular legislation or administrative rule or procedure would impose a burden on anyone's exercise of their religion so long as the purpose of the legislation, rule or procedure was not specifically to burden religion. So, for example, a zoning regulation that singles out houses of worship (or houses of the worship of a particular religion) for restrictions from specified areas would likely be found unconstitutional. But a restriction would be acceptable that would limit the number of people who may gather at one place in a given area would be considered acceptable, even if it would severely limit home Bible studies that some religious groups hold as vital to their ministry, since all groups that meet for whatever reason - even Tupperware parties - would be similarly restricted. Religions could not be singled out for restriction but general rules are general rules and if it burdens your practice of your religion that is just your tough luck. Perhaps you should find a religion easier to practice.
On an historic note, if this view of religious liberty had prevailed in the first part of the 20th century, Catholics, Lutherans, Jews, and probably Anglicans would have been out of luck in their use of alcohol in religious ritual under the Volstead Act. On a more contemporary note, the use of peyote in Native American religious ritual (not to mention eagle feathers) has been hotly contested and debated. (Tipping my hand, my sympathy is with the Native Americans here.)
Attempts have been made to support a more expansive view of constitutional religious freedoms. The most notable example of that is the 1993 Religious Freedom Restoration Act (RFRA) passed by Congress nearly unanimously and signed by President Bill Clinton. Since then the Act has been upheld as pertains to Federal laws and regulations but not to state law. Several states have passed similar laws. The greatest effect of this has been increased protection for Native American sacred sites and Native American use of peyote for religious rituals. It has also come into consideration in the various litigation concerning the ACA and especially the HHS contraceptive mandate.
Under RFRA a Federal law or regulation that has the effect of infringing on someone's religious freedom may be challenged because, in the words of the Act, “Government shall not substantially burden a person’s exercise of religion even if the burden results from a rule of general applicability.” In order to claim an exemption from a law or regulation under the Act, someone would need to show that their exercise of religion is being substantially burdened. In order to claim an exemption for the law or regulation from the Act the government would need to meet two tests. First would be to demonstrate that the law or regulation is necessary for the “furtherance of a compelling government interest.” (It cannot be something merely routine or just to make it easier for the government.) And further that there is no less restrictive means to accomplish that purpose.
Thus religion is not granted carte blanche to be exempt from any and every government law or regulation. But religion does hold a special place and may be restricted only by showing a serious need for the restriction. It is specifically not enough for the government to say that they are applying this to everybody and if it affects your religion more, too bad.
It seems to me that Brian is tending toward the more restrictive view of religious rights, namely that religion has no particular rights that the government needs to respect other than the right not to singled out for special restriction. He is certainly entitled to that view, and many certainly would agree with him. However, that is not the view that is currently enacted into law. RFRA is currently the Federal law and as ACA is a Federal program, enacted by Federal laws, it must function under the scrutiny of RFRA. It is not enough to say that the mandate for employers to provide free contraceptive coverage is a generally applicable law, like paying taxes, so religion is no reason to seek an exemption from the mandate. It is not even enough to say that those who object to the mandate are ignorant or misguided in their objections or that their religion is silly in objecting to the contraceptives. The question is not whether we like their religion but whether it is their religious freedoms are being burdened.
The challenge for the owners of Hobby Lobby, et al is to show that the contraceptive mandate constitutes a substantial burden on their exercise of their religion.
The challenge for the Federal Government is to either show that it is not a substantial burden or that they have a compelling interest in forcing employers to provide their workers with the contraceptives and that this is the least restrictive way to accomplish the goal of the mandate (which I presume is not to make employers jump through government hoops but to make contraceptives readily available to employees of larger companies).
No where in this legal mess is the goal of reducing abortions mentioned.
Dan