... The Court’s decision to incorporate the Establishment Clause was subject to scholarly criticism early on. The debate over the appropriateness of incorporating the Establishment clause revived in the early 2000s as a result of a series of concurring opinions by Justice Thomas.
The criticism of incorporating the Establishment Clause of the U.S. national Constitution and applying it to restrict state governments via the liberty guarantee of the Fourteenth Amendment arose because incorporation is based on a fundamental misreading of the Establishment Clause, and a misunderstanding of the nature of religious establishments. Justice Clarence Thomas initially questioned the application of the Establishment Clause to the states in the 2002 case of Zelman v. Simmons-Harris. He wrote that the Clause “originally protected States, and by extension, their citizens, from the imposition of an established religion by the Federal government.” He added: “Whether and how this Clause should constrain state action under the Fourteenth Amendment is a more difficult question.”
Thomas pushed further in 2004 in a concurring opinion in Elk Grove Unified School District v. Newdow, “I would take this opportunity to begin the process of rethinking the Establishment Clause . . . the Establishment Clause is a federalism provision, which, for this reason, resists incorporation.” He reasserted his position a year later in Van Orden v. Perry, observing that “the Establishment Clause is best understood as a federalism provision—it protects state establishments from federal interference but does not protect any individual right.”
The Establishment Clause serves two purposes: it both prohibits Congress from Establishing a religion but it also prohibits Congress from meddling with state religious establishments.Thomas followed and cited some notable scholars (not all of them conservative, for instance Akhil Amar) in the academy for the proposition that, as a federalism provision, the Establishment Clause resists incorporation. I think the argument is strong, but not quite airtight, for reasons I explain below.
In the comments, Dr. Ellis West chimed in:
The historical evidence simply does not support Prof. Rogers and Justice Thomas’ states’ rights interpretation of the establishment clause. See Ellis M. West, THE RELIGION CLAUSES OF THE FIRST AMENDMENT: GUARANTEES OF STATES’ RIGHTS? (2011), and reviewers unanimously accepted the book’s findings. Rogers’ interpretation is also based on the erroneous assumption, unfortunately perpetrated and maintained by the Supreme Court, that the establishment and free exercise clauses have different meanings. For the evidence that they were simply two different ways of saying the same thing, see Ellis M. West, THE FREE EXERCISE OF RELIGION IN AMERICA: ITS ORIGINAL CONSTITUTIONAL MEANING (2019).While I look forward to reading Dr. West's book, I am not convinced, yet at least, the two different clauses are "simply two different ways of saying the same thing." But I do believe there is something special about the two clauses that resists separating them.
And this is exactly what happens when the Free Exercise Clause gets incorporated to apply to state and local governments, but the Establishment Clause, because it's a federalism provision, does not. Interestingly, it was Professor Philip Hamburger who gave me this epiphany. Now, Hamburger does not think the Establishment Clause ought to incorporate; but rejects the doctrine of incorporation altogether.
So Hamburger's position is consistent. If the two clauses ought to rise and fall together because they can't be separated, his view is they fall together because nothing incorporates.
You might call this insight the "Siamese twin" thesis of the First Amendment's religion clause. When Hamburger explained it, he didn't use the Siamese twin analogy (I think you can attribute that to me), but rather invoked Wittgenstein. It was from a discussion Hamburger was having with fellow scholars of the religion clauses and he noted there were some Supreme Court cases where certain forces were advocating the term "religion" have one meaning for Free Exercise purposes, but another meaning for Establishment Clause purposes.
Hamburger noted from a linguistic perspective (I think that's when he appealed to Wittgenstein) such is a logical impossibility because even though they are two separate clauses, they use the term "religion" only once! The term "religion" is used in the Establishment Clause, but "thereof" in the Free Exercise Clause that relates back to the term in the Establishment Clause. That's why we call them "clauses"; they are part of the same sentence.
It's like two Siamese twins who share the same heart.