In Flast v. Cohen, 392 U.S. 83 (1968), the U.S. Supreme Court established that when Congress appropriated money for religious purposes, that taxpayers have standing to challenge that appropriation as an unconstitutional establishment of religion under the First Amendment to the United States Constitution.
Yesterday, in the case of Hein v. Freedom From Religion Foundation, Inc., the U.S. Supreme Court held that taxpayer standing to sue does not exist when the Executive branch spends money for religious purposes that could violate the Establishment Clause, if the Congressional appropriation that the funds come out of do not include a Congressional direction or suggestion that they be spent for religious purposes.
Chief Justice Roberts, and Justices Alito and Kennedy, joined the plurality opiniono. Kennedy concurred to remind the President that he has an independent obligation not to engage in the establishment of religion, even when no one can sue him over it. Justices Scalia and Thomas concurred in judgment, but would have overruled Flast and held that taxpayer standing is never sufficient to bring suit to enforce the Establishment clause.
Justices Souter, Stevens, Breyer and Ginsberg in dissent, would have upheld taxpayer standing any time that any branch of the government uses taxpayer funds to establish religion in violation of the First Amendment.
In short, the majority has left the Establishment Clause of the First Amendment as a right without a remedy in most cases. Justice Alito concludes his plurality opinion in the case by arguing that if there was a gross abuse of discretionary spending by the Executive branch, that Congress could swiftly step in, or that a basis for suit other than taxpayer standing could be found. But, his argument isn't terribly convincing.
The Establishment Clause is a limitation on Congressional power, not a privilege it jealously guards against Executive branch intrusion, so it has little incentive to limit the Executive branch and every reason to ignore Executive branch misconduct, if Congress shares the religious convictions of the Executive branch and would act on those Congressional religious convictions if the law did nont prohibit it from doing so. And, while it is possible to conceive of cases where a basis for standing other than taxpayer standing should be allowed, it is not obvious why this should be required. This ruling certainly leaves open the likelihood that in many cases there will be no remedy for executive branch establishment of religion, with the implicit consent, but not the direction, of Congress.
This is particularly a concern because there is no universal alternative to taxpayer standing in U.S. law. Most modern constitutions give someone, often a figurehead President or independent attorney general, or ombudsman, standing to enforce any actual constitutional violation, without regard to their personal harm. The U.S. Constitution, largely as a consequence of being one of the first democratic constitutions, does not. Moreover, since standing is an issue of Article III subject matter jurisdiction, it isn't clear that Congress has the power to create such standing, even if it wants to do so.