The Scientologists cut some sort of special deal with the IRS, a deal that is obviously bogus. The original dispute with the IRS was over Scientology being a religion at all, something that the IRS denied for a long time because the entire organization is run for profit.
Then suddenly the IRS reversed course and not only settled with the Scientologists but cut them a very favorable deal. It has long been rumored that they somehow got leverage over the people at the IRS and forced them to cut the deal.
The correct solution to this problem is to throw out the IRS / Scientology deal, not extend it to other religions.
Jay