From the opinion of Judge Brown (and this portion was joined by Judge Edwards):
Citing Citizens United v. FEC, the Freshway companies argue that corporations—religious or otherwise—are entitled to the full array of First Amendment protections, including the right to free exercise. They are not the only proponents of this position. See Hobby Lobby; see also Conestoga Wood. There is an appeal to this simple reasoning; after all, the free-exercise and free-speech rights are enshrined in the same constitutional provision, separated only by a semicolon.
Perhaps Appellants’ constitutional arithmetic, Citizens United plus the Free Exercise Clause equals a corporate free-exercise right, will ultimately prevail. But we must be mindful that Citizens United represents the culmination of decades of Supreme Court jurisprudence recognizing that all corporations speak. See Conestoga Wood. When it comes to the free exercise of religion, however, the Court has only indicated that people and churches worship. As for secular corporations, the Court has been all but silent.
Consider Bellotti—the progenitor of Citizens United. When the Bellotti Court declared “political speech does not lose First Amendment protection ‘simply because its source is a corporation,’” Citizens United (quoting Bellotti), it reviewed many cases in which the Court invalidated a state law because it “infringe[d on] protected speech by corporate bodies.” Bellotti. In other words, Bellotti crystallized a robust body of caselaw giving rise to the constitutional right of corporate political speech, which the Citizens United Court could rely on as a firm foundation.
No such corpus juris exists to suggest a free-exercise right for secular corporations. Thus, we read the “nature, history, and purpose” of the Free Exercise Clause as militating against the discernment of such a right. When it comes to corporate entities, only religious organizations are accorded the protections of the Clause. And we decline to give credence to the notion that the for-profit/non-profit distinction is dispositive, as that, too, is absent from the Clause’s history. Fortunately, we need not opine here on what a “religious organization” is, as the Freshway companies have conceded they do not meet that criterion.
Judge Randolph did not join this part of Judge Brown's analysis:
I do not join parts III and IV of Judge Brown’s opinion because I do not believe we need to reach the potentially far-reaching corporate free-exercise question. Other courts in contraceptive-mandate cases have “decline[d] to address the unresolved question of whether for-profit corporations can exercise religion.” The same approach may be used without deciding the rights of the Freshway Corporations because the government could enforce the mandate against the corporations only by compelling the Gilardis to act. Since “it is not necessary to decide more, it is necessary not to decide more.” PDK Labs. Inc. v. U.S. Drug Enforcement Admin. (D.C. Cir. 2004) (Roberts, J., concurring in part and concurring in the judgment).
We should be particularly hesitant to pass unnecessarily on such a complex issue. If secular for-profit corporations can never exercise religion, what of profitable activities of organized religions? If only religious for-profit organizations have a free-exercise right, how does one distinguish between religious and non-religious organizations? Why limit the free-exercise right to religious organizations when many business corporations adhere to religious dogma? See Mark L. Rienzi, God and the Profits: Is There Religious Liberty for Money-Makers?, 21 Geo. Mason L. Rev. (manuscript at 11-24) (forthcoming fall 2013). If non-religious organizations do not have free-exercise rights, why do non-religious natural persons (athiests, for example) possess them? If a corporate free-exercise right is recognized, in any form, there are equally challenging secondary questions. How should the beliefs of a religious corporation be determined? Can publicly traded corporations be religious? If so, do they take on the religions of their shareholders as a matter of course? If a religious corporation is sold, does it retain its religious identity? These questions, challenging in themselves, would confront us in different permutations across the diverse entity forms and organizational structures of the American business landscape.
UPDATE: I have generally avoidd citing second-hand commentary about these decisions, but this column by Emily Bazelon and Dahlia Lithwick contains several misleading (either by lack of understand, obfuscation, or some combination) claims about the role of Citizens United in the court's decision. The relevant text of the court's actual holding is cited above.