I'm not going to spend a lot of time on Hobby Lobby (PDF) itself. It is a profoundly flawed decision based upon a profoundly flawed statute, both of which desperately attempt to evade examination of their scifi foundations (and that's "scifi" as in "bad 1950s B-movie directed by Ed Wood," not "breathtaking work of imaginative fiction by Ursula K. LeGuin"; it's not a compliment)... and perhaps even their common foundations in the history of slavery in the United States.
On one hand, we have a reification worthy of Frankenstein: The corporation — or, at present, certain kinds of corporations, via a distinction unsupported in the corporation law of the relevant states — is now capable not just of suing and being sued, but of forming and holding religious beliefs sufficiently conduct-related to invoke the Free Exercise Clause of the First Amendment. Leaving the meaning of "free" for the past (and carefully ignoring my own history with that corporation in the 1980s when I was stationed in its hometown), Hobby Lobby has two legalistic-scifi implications that should disturb everyone.
Justice Alito's decision essentially amounts to reverse veil-piercing. The corporate formalities that justify limited liability for the shareholders have been reduced to the equivalent of an osmotic membrane, because now the corporation in question has taken on the very human characteristics of its controllers/owners — characteristics utterly irrelevant to its legal status, except as declared in this matter. The key question is this: Is there a principled reason that this must be a one way osmotic membrane, thereby restricting the limited liability of the owners? Consider, for a moment, that such a "Christian" corporation operates at full tilt on Fridays and Saturdays, but not at all on Sundays... and what that implies about its treatment of potential Seventh Day Adventist (sabbath is Saturday), Orthodox Jewish (sabbath is sundown Friday to sundown Saturday), and Muslim (sabbath is Friday) employees — and customers. More to the point, if the veil has been pierced to the corporation's benefit in allowing it frei und kostenlos anwendungen of its owners' religious beliefs — however firmly held — does that not expose the owners to personal scrutiny, and even liability, in the opposite direction? If so, it seems to me that the purpose of corporations (pooling of capital to enhance economic activity, incentivized by limiting risk via liability to the amount of the investment) has been rather thoroughly, and probably fatally, undermined. One must also ponder whether Hobby Lobby might apply to a hypothetical closely held foreign corporation that expresses firmly held religious beliefs.
And there one finds the far more disturbing implication: Not so much "personhood" as "citizenship." That's right: Paper people have more rights under the reasoning and rubric of Hobby Lobby than do brown people not born in the US. Hobby Lobby, after all, has free access to the courts to enforce its religious beliefs against the State. It can't be deported, have its assets confiscated, or be subjected to the whims of the Sheriff of MaricopaNottingham primarily related to its state of incorporation nation of birth. Again, I'm looking for a principled distinction that does not reduce to "but that's different;" the colors "blue" and "red" are different, but not so much to the colorblind. Unfortunately, I can't find it anywhere in Justice Alito's reasoning... or in the corresponding reasoning of those who oppose immigration reform. It all revolves around defining who is entitled to fundamental respect as a human and citizen, and may exercise the privileges or immunities of citizens of the United States... or be free of ownership by other persons.
In that respect, I think Hobby Lobby tries desperately to pretend that over two centuries of American history simply haven't happened, for the benefit of a set of very, very Caucasian citizens indeed. That this was not a conscious aspect of the Court's decision (or, indeed, of the litigation itself) merely takes it out of Jim Crow territory... and says that although the government-agency bus service can't discriminate, if the bus system gets completely privatized the answer might be different. For those who claim it couldn't go that far, I again ask for a principled distinction beyond "it's different."