Well, technically they're protesting the Church of Scientology and not Scientology itself. It's a very fine distinction, true, and not all of them are making it. But there are people outside of the CoS who practice scientology, and they're not the ones getting protested.

The difference between the crazed fundamentalist Scientologist and the mild-mannered Christian is that the mild mannered Christian won't attempt to utterly destroy you if you criticize their religion. The mild mannered Christian has not been trained in bullbaiting, either.