Constitutional horror: Clarence Thomas argues states can establish official religion - See more at:

[elleng]

3. 'Incorporation' is a serious legal issue,

has been for a long time, that is,

The incorporation of the Bill of Rights (or incorporation for short) is the process by which American courts have applied portions of the U.S. Bill of Rights to the states. Prior to 1925, the Bill of Rights was held only to apply to the federal government. Under the incorporation doctrine, most provisions of the Bill of Rights now also apply to the state and local governments.
Prior to the ratification of the Fourteenth Amendment and the development of the incorporation doctrine, the Supreme Court in 1833 held in Barron v. Baltimore that the Bill of Rights applied only to the federal, but not any state governments. Even years after the ratification of the Fourteenth Amendment, the Supreme Court in United States v. Cruikshank (1876) still held that the First and Second Amendment did not apply to state governments. However, beginning in the 1920s, a series of United States Supreme Court decisions interpreted the Fourteenth Amendment to "incorporate" most portions of the Bill of Rights, making these portions, for the first time, enforceable against the state governments.

http://en.wikipedia.org/wiki/Incorporation_of_the_Bill_of_Rights

Thomas (and others) call themselves 'originalists,' so it's not really a surprise that he takes this position.