Based upon my reading of the decision & the dissent:
1. It is not based upon the first amendment. This is the most important thing about the decision. The court DID NOT find that requiring a for-profit corporation to offer health insurance that includes contraceptive coverage is a violation of the free exercise clause of the Constitution.
2. So, then, what is it based on? It is based on a little known statute called the Religious Freedom Restoration Act, which was passed by Congress after Employment Division vs. Smith (a.k.a., the peyote/unemployment case). It was passed during the Clinton administration with overwhelming support.
3. What does this mean? Well, it means, in part, that the Supreme Court has finally declared that a corporation has essentially all of the rights of a person whilst still being permitted to avail itself of the limited liability of being a corporation. Which is sort of annoying and fucked up, but not much can be done about it given that this Supreme Court is pretty much always ready to provide a corporate handjob.
4. It also means that if you don't like the outcome, it isn't because the law was unconstitutional. And if you did like the outcome, you still can't claim that Obama was violating Hobby Lobby's constitutional rights, as the court acknowledged that but for the RFRA, the law would be CONSTITUTIONAL.
5. Beyond that, little can be predicted.
Could an otherwise qualifying, closely-held corporation owned by Scientologists or adherents to a faith healing sect invoke the RFRA to claim that the ACA requirement that they provide insurance that covers anything other than prayer (or whatever it is that Scientologists do) must not apply to them, and that, as well, they should not be required to pay the penalty that the law requires if they don't provide the insurance? I would say probably yes, although the Court is careful to state that their decision is narrowly applicable to only this situation related to contraception.
What about an otherwise qualifying, closely held corporation owned by Catholics. Could they invoke the RFRA to claim that the the entire contraceptive mandate should not apply to them, and that they should not be forced to offer coverage for any forms of contraception at all? Based on the reasoning in Hobby Lobby, I can't imagine how the court could avoid coming to that ruling without repudiating Hobby Lobby.
I've read the opinion, & much preferred the blistering dissent by Justice Ginsburg. If you don't like the outcome, the solution is to repeal RFRA. Talk to your Congressional representative.