Religion Dispatches reports on why companies cannot claim religion as a basis for rejecting parts of the Affordable Care Act:
... Since the [ACA] regulations were announced, the “contraception mandate” has been the cause of great controversy, as many non-profit religious organizations, including Catholic hospitals and religiously-affiliated colleges, have objected to offering birth control services through their insurance plans.
The narrow exemption in the original rules, which were not broad enough to cover Catholic schools like Notre Dame, is undergoing a re-evaluation. However, in addition to objections by religious non-profits, more than a dozen for-profit small businesses have filed lawsuits objecting to furnishing coverage for some or all contraceptive services because of the owners’ religious beliefs.
It might seem strange to claim that a corporation (or an LLC) has religious freedom rights separate from those of the “real people” who own or manage it. An Oklahoma federal district court, rejecting a challenge by Hobby Lobby Stores to the coverage mandate, thought it was, finding:
General business corporations do not, separate and apart from the actions or belief systems of their individual owners or employees, exercise religion. They do not pray, worship, observe sacraments or take other religiously-motivated actions separate and apart from the intention and direction of their individual actors. Religious exercise is, by its nature, one of those “purely personal” matters... which is not the province of a general business corporation.
Read more here.