The opening phrase of the First Amendment to the U.S. Constitution provides, "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof." The free exercise clause functions as an individual right with its purpose being to forestall personal religious harm. Its underlying principle is that in religious matters a person ought to be free of coercion caused by the government and thereby not made to suffer for cause of conscience. The function of the establishment clause is altogether different, for its purpose is to restrain government from using its powers to act on matters properly in the realm of religion. The resulting division between church and state impliedly acknowledges that the state is limited in its powers and that the churches retain sufficient breathing space to perform their work in society. The principle underlying this autonomy of the churches is voluntarism, with it consequence that inherently religious matters are under the auspices of the churches and not the state. This proper ordering of the respective competencies of state and church is best for the body politic because it avoids increasing factionalism along religious lines while reinforcing the idea of limited government, and it is best for the churches because it avoids corrupting religion. In addition to differentiating the two religion clauses, this shift to a structuralist establishment clause explains several longstanding puzzles about the clause: (1) Why the Supreme Court has carved out a special standing exception for federal taxpayers applicable only when asserting claims under the establishment clause; (2) Why the remedy (class-wide injunctive relief) in establishment clause cases is aimed more to negate the power of government rather than affording just victim-specific relief for the actual complainants; (3) Why establishment clause cases touching on religious doctrinal disputes lead to dismissals for lack of subject-matter jurisdiction when there is nothing in Article III of the Constitution that limits the power of the federal judiciary over such cases or controversies; (4) Why viewing the establishment clause as structuralist makes sense of the "two-definitions-of-religion" enigma, notwithstanding that "religion" appears only once grammatically governing both clauses; (5) Why the Court has struck down aid to religious schools reciting as one of its reasons that government aid would be harmful to the schools, while the religious schools themselves actively seek the aid and insist that they have waived any supposed constitutional safeguards to their religious integrity; and (6) Why the supposed "tensions" between the free exercise and establishment clauses ? as if the founders drafted an amendment that is internally contradictory ? go away when no-establishment is viewed as a power-limiting clause and free exercise as a rights-based clause.
Carl H. Esbeck, The Establishment Clause As A Structural Restraint: Validations and Ramifications, 18 J.L. & Pol. 445 (2002)