For the most part, the only difference between a "real religion" and a "cult" is longevity--a distinction that also applies to governments. If enough people believe in some form of the supernatural for a long enough period of time, we stop calling it a cult and start calling it a religion. Religions are cults that last.
One of the main reasons why it is a mistake to call atheism, freethought, or secular humanism "just another religion" is that unfettered inquiry is the basis of the secular worldview. Free inquiry is the mortal enemy of all controlling religions. Of course, secular ideologies such as Stalinist Communism can become controlling religions too, since they take on the imperviousness to evidence that is the ultimate expression of religious fanaticism. But that has nothing to do with the open-minded secularism, rooted in the Enlightenment, that is the basis of freethought today. Fear and loathing of intellectual challenge is the essence of all controlling religious factions, whether the God is called Stalin, Jehovah, or Allah.
Christian societies, of course, used to kill people for blasphemy. But time--and the rise of the great separation between church and state pioneered by the United States of America--has turned most of the Christian world away from the dogmas of controlling religion. But don't call this "real" religion, as distinct from a cult. It is simply religion moderated by secular knowledge and secular government.
Susan Jacoby, On Faith, 19. September 2007