A while ago I posted on Akhil Amar's views of the Establishment Clause and Equal Protection principles. His seminal book on the Bill of Rights notes that the original meaning of the Establishment Clause may make it hard if not impossible to incorporate. But he then asserts that because the Establishment Clause often acts like an equal protection clause, if the Court instead relied on the original meaning of the Equal Protection Clause on religious matters, the outcomes may not differ greatly were the Establishment Clause unincorporated. From his book:
Even a noncoercive establishment, [Thomas] Cooley suggested, violated principles of religious liberty and religious equality -- violated norms of equal rights and privileges. And once we see this, it turns out that the question -- should we incorporate the establishment clause? -- may not matter all that much, because even if we did not, principles of religious liberty and equality could be vindicated via the free-exercise clause (whose text, history, and logic make it a paradigmatic case for incorporation) and the equal protection clause (which frowns on state laws that unjustifiably single out some folks for special privileges and relegate others to second-class status). Surely Alabama could not adopt a state motto proclaiming itself "the White Supremacy State"; such a motto would offend basic principles of equal citizenship and equal protection. And so a law that proclaimed Utah a Mormon state should be suspect whether we call this a violation of establishment principles, free-exercise principles, equal-protection principles, equal-citizenship principles, or religious-liberty principles.
Now, exactly how the Equal Protection Clause could do what the Supreme Court currently has the Establishment Clause doing needs much more scholarly explication than is currently out there. Jack Balkin's recent post on the Establishment Clause and issues of standing shows, using an analogy to racial discrimination, the parallels between what the Equal Protection Clause does with race and the Establishment Clause does with religion. Keep in mind while reading the following that the Equal Protection Clause could the same with both.
Frankly, I've always thought this entire line of standing cases is silly. Standing to sue should depend on the nature of the underlying substantive right. In my opinion, the Establishment Clause does not simply protect citizens from certain spending decisions (although it does do that). It protects them from certain dignitary harms caused by the government's endorsement of one religion over another, of religion in general over non-religion, or of atheism over religion. In other words, the Establishment Clause requires the government to give equal respect to its citizens with respect to religious questions, both in its symbolic activities as well as in its expenditures of money. Thus, if the Government were to erect a large sign from general appropriations stating "There is no God," this would violate the Establishment Clause because it imposes a dignitary harm on religious citizens. (Note: not everyone agrees with this view of the Establishment Clause-- some think it only protects against government coercion, for example. Justice O'Connor championed the endorsement view, which the Court later adopted, and I think she was essentially correct.).
If my substantive theory of the Establishment Clause is correct-- and it is more or less the theory that the Court currently holds-- then then any citizen of the U.S. who suffers a dignitary harm by reason of endorsement in violation of the Establishment Clause has standing to sue, and any citizen of a state who suffers dignitary harm by reason of endorsement by a state has standing to sue. A person's status as a taxpayer is irrelevant because it has nothing to do with the underlying nature of the substantive right.
The Establishment Clause is not the only clause in the Constitution that creates dignitary rights. The Titles of Nobility Clause protects citizens from the dignitary harms caused when the government bestows aristocratic titles on someone else. So if the federal government decided to make me Lord Balkin, any other citizen should have standing to sue, and I wish they would! Similarly, I have long been of the view that although the First Amendment protects various forms of racist speech by private actors, speech by the government is in a different position: the Equal Protection Clause prohibits states from making official pronouncements that one race is superior to the other. It would also prohibit states from having "colored" and "white" signs on restrooms or water fountains even if the state never required or enforced segregation of facilities by law. (Indeed, in Brown v. Board, when the states assigned pupils by race, they also sent a message of White Supremacy; this was a dignitary harm separate from the material harms caused by forcing blacks to attend inferior schools. That is, as Chuck Lawrence once put it, Brown is both a segregation case and a case of racist speech by the government.). According to this theory, any citizen who belonged to a disfavored or dispreferred race would have standing to sue if the government engaged in racist speech.