Viva, hubby read me one theory (I think it's the same as Tybalt's, or at least how I understood Tybalt's theory) that in reality, Zion is just another level of the Matrix. When the Architect says that 99% of the people accept the Matrix as reality, well what do they do with the other 1%? They created an alternate reality that would perpetuate the idea of the Matrix, and allow for hope in that 1% that couldn't accept the "real world" as reality. Those in Zion *think* they are outside of the Matrix when really they are just in another *part* of it. Never occurs to them. Neo is able to stop the sentinals because he has come to realize how deep the rabbit hole goes.