I've never been clear on this, even after seeing all three Matrix films.
I understand that there's been a cycle where some humans don't do well and don't actually accept the Matrix and break out and start living in and building Zion. I know this cycle has been repeated, so what there is of Zion wasn't just built by the rebels in the current cycle. This also means Neo is only "The One" for this generation, that there's been previous versions of "The One," and after each rebellion, the cycle starts over again.
Why is this cycle necessary? When given a choice, do so few humans opt to stay in the Matrix that the Machines can't survive on the power they supply? Is there a reason the Machines and humans can't create an equilibrium, where those that want to live in Zion can live there, while all other humans stay in the Matrix?
Is there a reason the humans and machines have not agreed to a long term truce that allows free humans and Machines to live without interference and allows humans that prefer the Matrix to live in it and power the Machines?