If Hobby Lobby's employees share the owner's beliefs regarding contraception, then they won't use the coverage the company is required to provide. If their beliefs permit contraception, should the company oppose their religious freedom by denying coverage?
If your religious beliefs permit you to not cover procedures that you disagree with, what happens when a company whose founder believes that mental illness is caused by demons provides coverage for exorcisms instead of psychiatric care? What if they believe that all illness is caused by demons or sin and choose to provide no medical coverage at all? Should employees be bound by the religious beliefs of their employer?