Let me use the recent decision of the Supreme Court essentially “ducking” the Pledge issue as opportunity to update my thoughts on whether the Establishment Clause is properly incorporated against the states. What reignites this debate is that Justice Thomas, in his concurrence, held that based on an originalist reading of the First and Fourteenth Amendments, the Establishment Clause should not be incorporated.
Randy Barnett, someone with whom I agree almost all of the time, based on what he has written before, agrees with Thomas’s assessment. His argument is that the “privileges or immunities” clause refers to rights, both natural and positive. That’s what is incorporated—if we can’t find a particular “right” that the Establishment Clause would protect, then it doesn’t get incorporated. According to Barnett, the Free Exercise Clause does indeed refer to a "natural right" and as such ought to be incorporated. However...
In contrast, the Establishment Clause of the First Amendment describes neither a natural liberty right or "immunity," nor a positive individual right or "privilege" of citizens. It is simply a limitation on the power of Congress simpliciter. Therefore, the plain and original meaning of the Privileges or Immunities Clause of the Fourteenth Amendment has no relevance to the state establishment of religion. State endorsements of religions are not unconstitutional….
I responded to Barnett’s post and noted that Jefferson & Madison, (and other founders as well) were against state Establishments, that Madison tried to (and failed) to outlaw state Establishments in his first draft of the First Amendment, and that the Virginia Statute on Religious Liberty—which gives the Madisonian-Jeffersonian view on what the natural rights theory that undergirds our Founding has to say about religion & government—demands disestablishment as necessary to protect, “the natural rights of mankind.”
(BTW, Lawrence Solum has a link to an article by Professor Marci Hamilton’s and her view of the Pledge case, where she analyzes Thomas’s view on incorporation—her assessment is pretty much in line with what I have written. Anyway it’s an interesting article).
Then Timothy Sandefur objected to my analysis and defended the Barnett/Thomas view, and he did so while analyzing (and criticizing) the Virginia Statute’s rationale as to why establishments violate “rights”:
More importantly, can it really be said that the Establishment Clause protects a specific right, above and beyond the right not to be taxed for anything? That is to say, it violates our rights to degree X to be taxed, regardless of where that funding goes: if it goes to support sex ed, or the building of a post office, or for the arming of soldiers, or for the support of a church whose doctrines I despise, it still violates the same right, and to the same degree. For a Quaker to be taxed to pay for the army surely violates his conscience as much as my being taxed to support an established church with which I disagree.
Moreover he notes, "if we confine the discussion to the First Amendment itself, it’s not clear, either from the text or from principles of political philosophy, that the Establishment Clause either does, or can, protect an individual liberty—as opposed to simply limiting federal power."
Okay—so let me take another stab at why incorporating the Establishment Clause relates to protecting the “equal rights of conscience” as Madison would put it (it’s my opinion that the Free Exercise Clause and the Establishment Clause were necessary—that they go together—in order to protect our inalienable rights of conscience): Madison, et al. clearly believed that only a secular state, that is one that takes no stand on matters of religion, (one that effected “a perfect separation of ecclesiastical civil matters") could effectively enforce the equal rights of conscience. Somehow I don’t think that a “Christian Commonwealth” run by the likes of Roy Moore can effectively enforce the Free Exercise of Religion. Am I wrong?