From the nation's founding until today, the Constitution's protection of religious liberty has been seen as a personal right, inextricably linked to the human capacity to express devotion to a God and act on the basis of reason and conscience.
Business corporations, quite properly, have never shared in this fundamental constitutional tradition for the obvious reason that a business corporation lacks the basic human capacities -- reason, dignity and conscience -- at the core of the right to free exercise of religion. Obviously not "persons" in the usual sense of the word, these corporations are also not religious organizations, which have historically received some constitutional protection and are, in fact, given exemptions from the contraception mandate.
These businesses do not hire employees on the basis of their religion and their employees are not required to share the religious beliefs personally held by the corporation's owners. In all of American history, secular, for-profit corporations have never been understood to "exercise" religion -- have you ever seen Exxon Mobil in the pew next to you at church? -- and have never been protected by the right to free exercise.