When it comes to for-profit corporations, however, there are hints (and this is my modest prediction) that the Court’s refusal to inquire into the purpose or form of the corporation in the election law context may very well apply to the religious liberties context. The burdens placed upon corporations are likely to face the same scrutiny, regardless of the purpose or the form of the corporation. And that means, businesses like Hobby Lobby, under the Court’s precedent in Citizens United, would be treated as any other individual, church, or non-profit organization making a Free Exercise claim.
Today, the Tenth Circuit handed down an en banc opinion in Hobby Lobby Stores, Inc. v. Sebelius (PDF). Here's the majority's discussion of "Corporate and For-Profit Free Exercise Rights" (V.A.2.b of the opinion), which ties Citizens United and some other campaign finance cases in the Free Speech context into the Free Exercise context:
It is beyond question that associations—not just individuals—have Free Exercise rights: “An individual’s freedom to speak, to worship, and to petition the government for the redress of grievances could not be vigorously protected from interference by the State unless a correlative freedom to engage in group effort toward those ends were not also guaranteed.” Roberts v. U.S. Jaycees, 468 U.S. 609, 622 (1984) (emphasis added). Therefore, courts have “recognized a right to associate for the purpose of engaging in those activities protected by the First Amendment—speech, assembly, petition for the redress of grievances, and the exercise of religion. The Constitution guarantees freedom of association of this kind as an indispensable means of preserving other individual liberties.” Id. at 618 (emphasis added); see also Citizens United v. FEC, 558 U.S. 310, 342–43 (2010) (“First Amendment protection extends to corporations . . . [, and the Court] has thus rejected the argument that . . . corporations or other associations should be treated differently under the First Amendment simply because such associations are not natural persons.” (internal quotation marks omitted)).
Accordingly, the Free Exercise Clause is not a “‘purely personal’ guarantee . . . unavailable to corporations and other organizations because the ‘historic function’ of the particular [constitutional] guarantee has been limited to the protection of individuals.” First Nat’l Bank of Boston v. Bellotti, 435 U.S. 765, 778 n.14 (1978). As should be obvious, the Free Exercise Clause at least extends to associations like churches—including those that incorporate. See, e.g., Church of Lukumi Babalu Aye, Inc. v. City of Hialeah, 508 U.S. 520, 525 (1993) (holding that a “not-for-profit corporation organized under Florida law” prevailed on its Free Exercise claim); see also Terrett v. Taylor, 13 U.S. (9 Cranch) 43, 49 (1815) (Story, J.) (“[The] legislature may . . . enable all sects to accomplish the great objects of religion by giving them corporate rights for the manag[e]ment of their property, and the regulation of their temporal as well as spiritual concerns.”).
Because Hobby Lobby and Mardel express themselves for religious purposes, the First Amendment logic of Citizens United, 558 U.S. at 342–55, where the Supreme Court has recognized a First Amendment right of for-profit corporations to express themselves for political purposes, applies as well. We see no reason the Supreme Court would recognize constitutional protection for a corporation’s political expression but not its religious expression.
There are more citations in other opinions of other judges, if you're interested in reading.