Quite simple. Matrix is the system created by God ( our earth, we, life etc). God put some rules we should follow them. BUT, the majority of people including here Satan, masons etc don't like being controlled and told what to do and what to follow. They are against this system ( Matrix) and they are fighting against it. From the beginning they know that their fight against God (SUPER MACHINE) is impossible, but they want at least to change his mind and let them live in peace without rules, constrains. That's MATRIX all about.
A very faimous quote from this movie:
“The Matrix is a system, Neo. That system is our enemy. But when you're inside, you look around, what do you see? Businessmen, teachers, lawyers, carpenters. The very minds of the people we are trying to save. But until we do, these people are still a part of that system and that makes them our enemy. You have to understand, most of these people are not ready to be unplugged. And many of them are so inured, so hopelessly dependent on the system, that they will fight to protect it.”