The Matrix is a movie about superstructure. You have the material world where humans are kept in pods producing value for the machines and you have the Matrix where they think they live their lives, which is built and maintained by the ruling machines to contain them. The real Earth where machines rule with an iron fist is the base, and the Matrix is the superstructure.

The Matrix is presented to mankind as a natural, material fact, but it isn't. The machines are able to fuck with the Matrix to pursue their own ends within it because it's a mental construct. Superstructure is malleable, and the ruling class will bend it to maintain their power.

Something about living in the Matrix rubs humans the wrong way. Of course it does. It's built with someone else's interest in mind at humans' expense. But they don't know what it is that's bothering them because the controlling Matrix is the only thing they've ever known, it's Normal. But little by little, people who can't abide the Matrix wake up. They realize that it's fake, that things don't need to be the way they are. They learn that they themselves can manipulate the Matrix, and they do so to pursue their own purpose - human liberation.