I am posting this in the hope that it will discourage more email making this same point:
I’m sure you’ve received quite a few replies on this, but one more couldn’t hurt.
At the end of Reloaded, the Architect reveals to Neo that Zion has been destroyed six separate times. Due to the systemic anomaly (Neo is the anomaly), human are gradually freed from the Matrix. At first, only a few are freed, but eventually there is a snowball effect as more and more humans free themselves from the Matrix.
The Machines feel there is a “critical mass” which, when reached, action must be taken. Once 250,000 humans are freed of the Matrix, they destroy Zion in order to halt the snowball effect.
Because the Matrix is not mathematically perfect and humans are inherently flawed creatures, he implies that some humans will always be trying to wake up from it, and a tiny minority succeed. Zion seems to be the method of controlling those humans who are awakened from the Matrix.
Whether or not Zion is simply a matrix within a matrix is a matter of debate. But the solid point is that 250,000 humans are the most the Machines allow to be freed at one time. Once that number is reached, they wipe them out and start again. So, every hundred years or so, 250,000 humans are killed while tens of millions continue to live unaffected and unaware of the Matrix.
Hope that helps.