I can't tell exactly whats going on here so I might be WAY off the mark. It sounds like the federal government initially said Scientology wasn't a "real" religion, so Scientology sued and was specifically named as being tax exempt. Now other people are claiming that Scientology is benefiting unfairly.
I don't know exactly what going on but heres the deal. The government cannot favor anyone religion, thats the establishment clause. Personally I'm not sure why religions are tax free but thats a different debate. The question is does this law favor scientology or simply put it on the same standards as the others? If its just putting them in the same category as the other cults, er religions then why should it even be named? If its putting them in a different category then other religions wither for better or worse then its illegal. I'm no judge but that seems simple, now the only question is if this puts scientology into a different tax group than other religions, for that you'll need someone who knows what they're talking about.
UPDATE: Commenter clears things up, Thanks!