No one heard much about Scientology before Tom Cruise. Unfortunately he did not help boost the image of the fake religion. His nonsense and odd behavior made people sceptical and they began to associate everyone in Scientology with Tom Cruise. Scientology itself cannot be taken seriously and Tom Cruise has proven that.
Tom Cruise jumped on Oprah's couch and with that jumped into Scientology infamy. After that, Cruise lost a lot of acting jobs because he was seen as unstable. For the same reason, he has been a blight to the image of Scientology. People don't want to sign on for something strange or erratic.
For better or for worse, Scientology is largely seen as a money-making operation rather than a legitimate religion. Furthermore, the fact that its doctrines are seen as so outlandish that South Park could find material to make fun of it with suggests that even if Tom Cruise had nothing to do with Scientology, this belief system would still be looked down upon.
No, Tom Cruise has not ruined Scientology's image. While he seems to have been placed in a strategic position to represent Scientology, Tom Cruise does not represent the entire religion. His words and actions are merely one big example of what is both tolerated and likely expected of the religion and its followers.