Not sure whether there is a universal definition of religious freedom, but here is mine. Religious freedom means no persecution, no discrimination, freedom to worship, and freedom to speak and spread word.
It does not necessarily mean freedom from evenly applied taxation, nor does religion prevail over the public interest. Except for clerics, employment laws regarding discrimination should apply, and requirements for health insurance should prevail over religious doctrine. And this should true for churches as well as for more secular activities such as hospitals and universities. Requiring coverage of contraception as a matter of public policy does not endanger freedom of religion in this country.
Remember the legal prohibitions regarding polygamy and use of hallucinatory drugs.
Bonus thought: pharmacies, which are licensed to serve the public, should not be allowed to refuse to fill prescripions because of religious objections of owner, manager, or employee.