"But on Monday morning, the apocalypse didn’t come. In fact, quite the opposite: In its ruling for Hobby Lobby, the court—in an opinion authored by arch-conservative Justice Samuel Alito—explicitly stated that RFRA could not be used as a “shield” to “cloak … discrimination in hiring” as a “religious practice to escape legal sanction.” RFRA doesn’t permit employers to break a law when there is a compelling government interest backing that regulation, and, according to Alito, the government “has a compelling interest in providing an equal opportunity to participate in the workforce.”
Alito cites racial discrimination in his opinion. But Justice Anthony Kennedy, in a concurrence, cabins the court’s ruling even further, making clear that the majority isn’t rewriting RFRA (or the First Amendment) to protect anti-gay discrimination.
Kennedy denies that the opinion is a startling “breadth and sweep,” noting that this case could easily be “distinguish[ed] ... from many others in which it is more difficult” to strike a balance between legal regulations and “an alleged statutory right of free exercise.”
While religious liberty may permit employers to exercise their own beliefs to a point, “neither may that same exercise unduly restrict … employees in protecting their own interests.” Translation: This case is about birth control and nothing more—and as a general rule, employees still have a compelling interest in most laws that protect their rights."
The Hobby Lobby ruling is good for gays and doesn't allow discrimination.
The linked article further goes on to discuss how the majority in that decision took on Ginsburg's direct question of whether religious liberty allowed anti-gay discrimination (& not just in employment): “Would RFRA require exemptions in cases of this ilk?” she asks. “And if not, how does the Court divine which religious beliefs are worthy of accommodation, and which are not?”