I have a hard time with that. Religious bigotry sucks, and who am I to say that Scientologists have any less claim on higher truth. They have a rep for doing some scary stuff. So do most of the big religions.
I guess, people are pretty much horrible as a giant chunk. Religion is supposed to fix that on an individual level, but sometimes, as a giant chunk, religious people can sometime still be pretty much horrible.
On a subtler level, I have problems with the cash changing hands, and the methodology. I ran into of a group called Landmark a couple years ago. Google 'em up. They have similar practices to Scientology, but without the Thetans. Here's how I ended up in their midst. Some friends of mine invited my wife and I to an informational night. We sat in on an uplifting group where people talked about how they were taking charge of their life. Then my wife and I went off into a side room with the local muckymuck, and two other people. There were 5 seats in the room. Three tall stools, and two normal chairs. The stools were in a triangle around the smaller chairs, two Landmark people sitting behind us, and 1 landmark guy right in front of us so we had to crane our necks up at them. Then started an hour and a half of hard selling.
By the end, my wife and I had handed over $1400 for the Landmark forum, and some other Landmark courses. I went home, and sat at my computer, and slowly went "HOLY CRAP!" They'd gotten me. I called them and said that I wasn't interested in Landmark, and that I wanted my check back. They said they couldn't give my check back, and that would have to go through the NW Regional coordinator who was in Seattle. A little research showed that they didn't have an office, but a rented cubicle. I called, left a message, and then put a stop on the check through my bank.
They turned around and had the friends that invited me to the informational meeting call me, and shake me down as to why I didn't have the integrity to go to the Landmark forum, and to follow through on my word. Nice... nice.
Fair or not, from what I've read, Scientology operates a lot like Landmark/Est, which is alone enough to make me REALLY wary of them, especially with the added religious component.