I understand that those who practice scientology see it as a religion, but anyone with a clear head can see it's a steaming pile, and not in the same sense as other major religions.
It's wrong for the German government to discriminate in this case, but anyone arguing that scientology is a "religion" on the same level as the other major religions needs to seriously rethink his definition of "religion". This is a thin layer of philosophical nonsense, covering a largely unethical and essentially criminal organization. The religion ignores the tradition and movement towards equality and tolerance, instead promoting distinction between its members and the general population, and pushing its own goals above even its own followers.
You can argue other religions do this too, but the difference is they are borne of centuries-old traditions that have slowly changed with the times, have changed the times themselves, and are still in the process of adapting themselves to the more liberal modern world. This "religion" was borne of that progressive world, and subsequently has denied central aspects in in order to establish what is effectively a pyramid scheme. Not to mention Jesus never talked about setting up a scam religion in order to make money (of course, it wouldn't be mentioned in the bible, but no accounts exist that would have been jumped upon by critics of the time, nor does it reflect the nature of his movement anyway).
Comparing scientology with Christianity in the respect that it is just being martyred as a new kid on the block is absurd: it is being attacked because it is engaging in illegal activities and attempting to establish an authority that is antagonistic to rationalism, democracy, and the rule of law.
And comparing this reaction to one against Islam because of an extremist element belies an understanding that extremist elements = Islam. It is mostly a religion of peace and brotherhood. Of course you wouldn't go after all of Islam for a few bad apples.
And that its followers should be allowed to find their own movement to follow like sheep, fine people should be free to do that. When their movement, however, engages in highly unethical hypnotic techniques used to abuse their followers and take their money and sanity, it crosses the line between harmless faith and criminal organization.
It is a testament to the power of PR and money on common sense and reason. A perfect religion for the modern era, but only in that it encapsulates the worst thereof.