When an apparently neutral government regulation burdens an institutionalized person's ability to practice his religion, RLUIPA requires the government to prove that the regulation is necessary to further a compelling governmental interest. This "strict scrutiny" standard is very difficult to meet; more important, it is more than the Supreme Court has said the government has to meet under the Free Exercise Clause of the First Amendment. The Court of Appeals for the Sixth Circuit had held that RLUIPA violated the Establishment Clause (separation of church and state) because it singled out religious activity for special protection, as opposed to other constitutional rights like free speech. The Supreme Court rejected that analysis.
A couple of years ago, I wrote about RLUIPA's history and criticized a previous Sixth Circuit panel for striking down the statute.
Meanwhile, if you want to understand why Bush's admiration for Clarence Thomas scares liberal believers in judicial restraint like me, read Thomas's concurring opinion in yesterday's case. Thomas reiterates his belief that the Establishment Clause does not apply to the states; in other words, Rhode Island could make the Roman Catholic Church the official state church, and Alabama could install the Southern Baptists as the Church of Alabama. Thomas thinks that the Establishment Clause was originally intended to protect state-established churches by preventing the federal government from establishing a national religion ("Congress shall make no law...."), so that when the Bill of Rights was applied to the states after the Civil War when the Fourteenth Amendment was passed, it wouldn't have made any sense to think for the Establishment Clause was part of what was meant to be into have been included. In other words, the Free Speech Clause properly restricts state governments, even though it originally applied only to the feds, because the Fourteenth Amendment (which does apply to the states) was understood to incorporate that clause; but the Establishment Clause still applies only to the feds because the Fourteenth Amendment wasn't (and logically couldn't) have been understood to incorporate that clause. This "originalist" analysis of what the Establishment Clause and the Fourteenth Amendment were understood to mean when they were adopted is not shared by the Court's other supposed "originalist," Antonin Scalia.
Now that the appellate courts are split, we might see the Supreme Court get involved yet again. If it does, I hope the Sixth Circuit's view gets crushed. I'm quite hawkish on Establishment Clause issues. I think that people who say the courts are anti-religion when they rule against school prayer or putting the Ten Commandments into public buildings are totally wrong. But this really does seem anti-religious to me. The problem with school prayer and Roy's Rock are that they are instances of the government's expressing religious faith. I think the government should be neutral, which means both refraining from endorsement of religion and making sure not to interfere when private individuals practice their religion. So the school P.A. shouldn't broadcast a prayer before the homecoming game; but teachers also shouldn't harrass students who get together between classes to pray. Here you have Congress saying the government ought to take some extra care not to trample on religious practices when it's not really necessary, and a court says that's a no-no.
Damned Clinton judges.
Thomas's concurrence also repeats his quite radical views on the scope of Congress's power under the Spending Clause and the Commerce Clause. Thomas would return us to a pre-1937 understanding in which Congress can regulate only the movement of goods across state lines, but not the manufacturing of those goods. That was the doctrine that led an activist Court to strike down national legislation on subjects like child labor and provoked FDR's terrible Court-packing plan. Thomas also thinks the Court should crack down on Congress's technique of attaching conditions to money it gives the states; here, RLUIPA applies to state prisons only because the states accept federal money to run the prisons.
During the squabbles over judicial appointments, bear in mind that Thomas and Scalia are the two judges whom Bush cites as models for his own appointments. Given Thomas's activism and aggressive approach to striking down Acts of Congress (Scalia being a bit--but only a bit--less gung-ho), you can understand why folks like me laugh bitterly when Bush lauds these guys in the same breath in which he says he wants judges who "don't legislate from the bench" and "interpret the law rather than writing it" and "believe in judicial restraint."