Scientology scares mainstream religion because it highlights a broken part of the human brain, that all religions exploit. L. Ron Hubbard, a notorious con man, and fraud, is absolutely no different than the leaders of many other religions. This scares mainstream religion, because people may eventually wake up to the fact that their religion is just as stupid as Scientology.
People want hope, and highly intelligent con artists have been exploiting the world for most of civilization. Which con man, and which religion, has largely been "an accident of birth" according to Richard Dawkins, who of course states the obvious. People mostly pick their religion because they are born into it, and become brainwashed.
Scientology is just one of the new "religions". If you look at the history of Mormanism you will see a truly disturbed psychotic in Joseph Smith, who, as a result of visions from God, started a branch from mainstream Christianity. In hindsight, Mormanism, is just about as wacky as Scientology, and the founders of both religions have much more in common than not. Both were accused of fraud, both were con men, and both liked taking money and women from other people.
Mainstream religions like Christianity, and Catholicism, should not be laughing and poking fun at either Scientology or Mormanism though. Lets take a look at their problems. Starting with Catholicism, we can see an ancient history of both murder and mind control, a newer history of hiding sex abuse. Evangelical Christianity too, is fraught with trouble and hypocrisy, and you wonder how people can belief ANY religion.
Finally, if these religions don't scare you enough, take a look at the violence, hatred and mind control that springs from Islamic Extremism. Many members of Islamic religion are peaceful, but others are clearly being brainwashed by highly intelligent and manipulative con artists in that religion.
All of this scares "mainstream" religion, because it may cause more and more people to question not just Scientology, or Islamic Extremism, but Christianity and Catholicism as well. If millions of people can be brainwashed by a 3rd rate Science Fiction writer in the 1950's, then maybe BILLIONS of people are being brainwashed by the other religions. This is why mainstream religion is scared by Scientology. Scientology is so delusional, it just might cause people to question if their religion is any different.