Personal theory - a good open flamewar every once in a while gets it out of people's systems.
Hmmm, the Zion control theory...:hmm:
However, a Machine program named the Architect, the creator and manipulator of the Matrix, manipulated the situation so Zion served as a control for the survival of the program in two ways. Firstly, the Machines could allow any humans who did not, or could not, accept the Matrix for what it was to live in the physical world without having to recapture them (this reduced dissent within the Matrix's population and prevented an exponentially-growing rejection rate from its population from causing entire "crops" of humans to die out, reducing power output).
Essentially, Zion was allowed to exist by the Machines as a giant pressure-release valve on the entire system, allowing the humans that realized the Matrix wasn't real (statistically, only a fraction of 1% of the whole human population) to be conveniently removed and isolated. Secondly, the Architect would periodically destroy Zion and its inhabitants as part of a deal coercing the One into reinserting the "Prime Program", a program code required to maintain the Matrix, allowing the Matrix to continue and Zion to be rebuilt by chosen survivors without memory of the destruction.
Rest assured we, your benevolant ARM/x86-hybrid based machine overlords, will resist the urge of enacting the Prime Program...for now at least :sneaky: