Since Zelman v. Simmons-Harris (2002), the Supreme Court has made clear that school choice programs, which financially support parents' sending children to private schools, may include religious schools, without violating the Establishment Clause—just as university scholarship programs (such as the GI Bill and others) may be used at religious institutions alongside secular institutions without violating the Establishment Clause. But must they include religious schools on basically the same terms as secular schools, in order to comply with the Free Exercise Clause?
In today's decision in Carson v. Makin, the Supreme Court said yes, by a 6-3 vote (following two earlier cases, Trinity Lutheran Church v. Comer and Espinoza v. Montana Dep't of Revenue, that had pointed in this direction, and distinguishing another earlier case, Locke v. Davey, that pointed in the opposite direction). The government need not have school choice programs, of course; it is free to just fund education at government-run public schools. But if it decides to support private education as well, it must do so without discriminating against religious schools.
Here are excerpts from Chief Justice Roberts' majority opinion, joined by Justices Thomas, Alito, Gorsuch, Kavanaugh, and Barrett: