The Matrix is a simulated, near-perfect reality.
It's one flaw; choice.
Simulations showed that, if subjects within the Matrix would have the choice to stay or leave, even if only subconsciously, 99% would choose to stay.
Take away this choice, and it shall result in a catastrophic system crash.

Every single subject in the Matrix had, at one point in their lives, a choice to either stay in the Matrix, or to unplug from it, and live in the 'real world'. As shown in simulations, 99% of all subjects chose to stay plugged. They don't recall ever making this choice, but they made it - subconsciously.

After recent events, it is now an open choice. Every individual may plug in or plug out at any given time.