The Matrix Theory is Like God
I'm pretty sure that every atheist has probably come into heated contact with a faithful theist at one point or another. As much as one party believes in the superiority of their beliefs, neither side can ever really win. Why? Because the existence of a Supreme Being cannot be proved or disproved. To argue over something as subjective and faith-based as the possibility of a God is to enter an endless tug-of-war. The atheists claim that God cannot be because there is no definitive proof of her/his/its existence. If God were to walk up to an atheist one day and prove beyond all reasonable doubt that God was God, that atheist would probably become a theist because evidence would exist.
The theory of The Matrix is very similar. That we are controlled by human-eating machines for food on a rotting dystopian Earth is certainly possible - however, the theory cannot be proved or disproved. And thus, like the God question, believe whichever makes you happy.
As an aside, it is very easy to invent these kinds of world-warping theories and scare people with them. It's even more entertaining if you make them completely plausible; that is, if you make the theory fully compatible with our current understanding of the world. For example, I could say that the universe is really floating on a giant pan of milk, but you can't tell because the pan is invisible, and you can't see the milk because it's made of rays that fall outside our currently-known spectrum of waves and we can't detect it yet. Sure, the milk theory is possible and plausible with our current understanding of the universe, but since it can't be proved or disproved the theory is pretty much useless.