Carlos brought this up in his thread about whether or not Neo should fear anything inside the Matrix.
Neo essentially has the power to destroy the Matrix from the inside, but by doing that he would kill everyone hooked into it.
As a side note, a possible reference from the bible is mentioned in the TIME magazine article - the number 314, which shows the most relevance to this movie in the third book of
Exodus
The sections 3:13 and 3:14 are fairly significant, as they show Moses being told that he is something equivalent to "the one". This leads me to believe that Neo is infact a symbol for Moses and that the only way to destroy the matrix is for Neo to
"...stretch out my hand and strike the Egyptians [Machines] with all the wonders that I will perform among them. After that, he will let you go. "
I'm guessing "He" is the architect mentioned in the TIME Magazine article.
It also shows a possible reference to Descartes most famous quote "I think therefore I AM", which could prove to be a way to destroy the machines. Destroy their ability to think, and you destroy their existance. It would be possible to leave the humans in the Matrix, but at the cost of traping them in some sort of continuous loop (Revolutions?)
Hell, I could be way off, but maybe someone will agree with me.