In Arizona Christian School Tuition Organization v. Winn (09-987), the Court held that plaintiffs challenging an Arizona law providing tax credits for contributions to charitable "school tuition organizations" lacked standing to pursue that claim under the Constitution. The plaintiffs had argued that, as Arizona taxpayers, they are being compelled to participate in the financing of religiously-affiliated schools, and that this violates the Establishment Clause of the First Amendment. In an opinion joined by Chief Justice Roberts and Justices Scalia, Thomas, and Alito, Justice Kennedy concluded that, because the method of financing involves tax credits rather than tax appropriations, the plaintiffs haven't been harmed in a way that gives rise to an actual "case or controversy" under Article III of the Constitution. Unlike a situation where an individual pays $1 in taxes, and some portion of that $1 is appropriated to finance sectarian religious activity, this case involves contributions by private individuals, which reduce their tax liability under Arizona's law. For the majority, this is a meaningful distinction because no individual is compelled to contribute his or her tax dollar to a sectarian institution.
As Justice Kagan made clear in her dissent - which was joined by Justices Ginsburg, Breyer, and Sotomayor - the general principle that taxpayers lack standing (simply by virtue of paying taxes) to challenge government action is accepted by all members of the Court. However, the question is about the extent to which an exception to the general principle applies to challenges of government action under the Establishment Clause. Prior Supreme Court caselaw, particularly a case called Flast v. Cohen (1968), established that tax appropriations for sectarian religious activity do give rise to taxpayer standing under the Establishment Clause. The majority, in distinguishing tax credits from tax appropriations, placed limits on the ability of future plaintiffs to rely on Flast in challenging governmental activities alleged to violate the Establishment Clause.
According to Justice Kagan and her fellow dissenters, the majority's holding "devastates taxpayer standing in Establishment Clause cases." This is because future legislators wishing to provide subsidies for sectarian religious activity need only draft tax provisions as credits rather than direct subsidies in order to eliminate taxpayer standing. Because there is no economic distinction between a tax appropriation and a tax credit, the minority did not believe that a legal doctrine of such crucial importance should hang on the difference.
Justices Scalia and Thomas, on the other hand, while concurring in the outcome, wrote separately to argue that Flast should be repudiated as a "misguided decision." They, in other words, do not think there should be any exception to the general principle that taxpayers lack standing to challenge governmental activity in Federal court.