I am trying to find the specific rights you are referring to in your post. Here is what I come up with:
1) Christian symbols being disallowed on federal government property.
2) Disallowing the use of peyote in religious cerimonies.
3) The discussed but unexecuted change in tax exemption for churchs
4) The possible use of anti terriorist measures against churchs.
What I see is that 3 and 4 may be a possible future erosion but haven't happened.
Would you agree that 1 and 2 are the ones your are putting forward as eroded rights? Did I miss any?