There are a couple reasons for this. A bit of background is needed though. The Constitution sets up the means for dealing with Native tribes as through treaties. Article 1, Section 8 lays this out, and places Indian tribes among foreign nations. The Supreme Court, with Chief Justice Marshall (known as the Marshall Trilogy) clarified the relationship by deeming Indian tribes as domestic dependent nations. This did a few things. It again clarified that the federal government had the sole authority to deal with the tribes, and that the relationship between the tribes and the state was like one of a guardian and its ward. Finally, in 1924, with the Indian Citizenship Act, Indians were granted U.S. citizenship. Before that, they were not citizens and the Constitution didn’t necessarily apply to them. Even after that, because of the special relationship that Indian Tribes had with the U.S., as set out in the Constitution and Supreme Court, a different set of laws was also in play.
There is more to it though. What constitutes a religion, or religious act has been up for debate. It wasn’t until 1978, with the American Indian Religious Freedom Act was passed, which expanded the traditional definition of what constituted a religion. But that didn’t really solve everything either. In 1993, the Religious Freedom Restoration Act was passed by Congress, and read in part that “laws ‘neutral’ toward religion may burden religious exercise as surely as laws intended to interfere with religious exercise.” That was amended by the Supreme Court in 1997 with the City of Bourne v. Flores decision which really was the Court reasserting their authority to interpret the Constitution.
So it boils down to two things. First, American Indians have a special relationship with the United States, and that causes different sets of rules and practices to be in play. Second, what constitutes religion has been an ongoing debate that has reinterpreted many times.
