I’ve never been a fan of the Court’s holding that a neutral statute of general application is constitutional even if it imposes a significant burden on a religion. There is decent evidence that this was contrary to the original understanding of the Fourteenth Amendment, Michael McConnell wrote a terrific article making the case against the decision when it first came out, and others have offered plenty of criticisms.
Recent events, though, show why Smith rests on a questionable understanding of the First Amendment. When a neutral and generally applicable employment discrimination statute was applied to churches, the Court adopted a “ministerial exception” and distinguished Smith. When HHS adopted a rule about contraceptives and made no exception for Catholic institutions, howls went up that this violates religious freedom. And those howls are right. Now I’ll grant that you could say that this is just a matter for Congress or state legislatures. (In other words, religious freedom could mean more than what the Court says is constitutionally required, though that doesn’t explain the “ministerial exception” case.) But I think that the Catholic organizations upset about the new regulation ought to have a constitutional claim. But they don’t.