Actually, The Matrix hearkens back to an ancient (if widely rejected in modern times) belief of metaphysical philosophy: Idealism.

Originally introduced by Plato in his The Allegory of the Cave, Idealism is (in very basic terms) the concept that there is only the mind, and that everything that is not the mind are merely sensations of the mind. Plato makes analogies to this cave as the place where people see nothing but shadows, and to become enlightened, one must escape the cave and have true experiences. Upon leaving the cave, one cannot easily return to enlighten others. The others will be caught in their own illusions of reality and consider the return a threat. People historically do not take well to having their belief system shaken up. Therefore, what would happen to the returning enlightened? He would at best be ridiculed by the residents of the cave. At worst, killed.

Neo being "awakened" is merely his escape from this cave. It makes for an interesting story, and one of the few blockbuster movies that actually takes a tenet of philosophy and uses it as the foundation of its plot.

There's really nothing all that sinister about it, unless you are exceptionally paranoid. And it made for a great movie. Idealism is kind of a silly idea, if you understand the arguments that make it silly, but that belongs in a different node.