Usually people distinguish a cult from a mainstream religion based on the level of control that the movement exerts over its members.
I'm not defending Scientology, but the line between "cult" and "religion" seems a bit blurry.
http://en.wikipedia.org/wiki/Sociological_classifications_of...
You can also think of it in terms of 1 Corinthians 13:11. Maturity, and the turning of generations, does something to an organization. Christianity began as an apocalypse cult, after all, promising hope of the afterlife for the downtrodden; it wasn't until Constantine was converted that it started to learn how to be a state religion; and not until Martin Luther and Henry VII did it learn to be just a religion. (The exile into Babylon and the dissolution of the Caliphate had similar effects on Judaism and Islam.)
In other words, they were forced to let go of their control simply because of historical circumstance. Straight through World War 2, the Vatican continued to exert a very strong influence on European nations... because the Pope was everyone's ambassador, even if he could no longer threaten excommunication with meaningful clout.
Scientology has not had these experiences. It is young and not officially descended from any known religion, so "sect" would be an incorrect term except in cases where you consider the entire whole of Judaism or Christianity a sect. It is dominated by personality cults, from the original of L. Ron Hubbard to its scheme of hooking celebrities to be spokespersons.
With that said, there may be a feedback-theory reason why these things often connect. In the case of governments, for example, bureaucracy allows you to marshal much vaster quantities of resources, especially for your military: so as we look for a positive feedback loop, the most successful governments were probably bureaucracies. (Yes, I would also classify evolution by natural selection as a feedback theory.)
It may therefore be the case that there is a competition for a limited believership and the religions which control their believers most tend to grow themselves in this competition. If you want an interesting perspective on what Anonymous is doing, it is trying to increase the cost of religious control, to the point where the feedback goes from positive to negative. If each exertion of control (however that is defined) tends to lose believers rather than gain them, then religions will either have to adapt to a policy of less-control, or else will naturally die out due to negative feedback.