The Matrix is basically a Frakenstein story. Man creates a living creature and plays God. In this case Frakensteins monster is AI, a single consciousness. The monster sees us as inferior and tries to destroy its creater. And it does so.
I found some essays that people have written on the Matrix and one that was interesting is that the machines have been very humane in their dealings with the humans. In fact they even tried to create a paradise for them but it was rejected. They went through three matrixs before they found one that was accepted. They didn't have to do that. They could've just kept us in a coma while they harvested our energy. But they were willing to live in harmony while both sides benefited. The machines wanted survival and needed us and we destroyed our planet and the matrix would allow us to live a perfect life without ever knowing the difference. So everyone wins. They don't mention this in the movies. The agents are just there to keep the peace and to make sure there's nothing to cause problems for the matrix. The Agents don't kill anyone unless they are a threat to the system but even then, the dead are fed to the survivors so there is no waste.
Considering how we depend on machines for survival and many of us abuse those very machines that we depend on (look at what people do with their cars!) I think the machines are more humane than the humans are. They are willing to live in harmony in a mutual beneficial relationship. In the Matrix, EVERYBODY WINS.
Now there's a spoiler here! When Neo meets the Architect he is told that the only Matrix that was accepted was one that not only had some strife but one that allowed CHOICE. It was still perfect in the eyes of the architect with the exception of a random "anomoly" where a random person will kind of assimilate some of the source code of the matrix and be able to alter it and control it as he sees fit. That person will then have a choice to walk through door #1 and strip the code from his essence, the matrix will reabsorb the anomolous code and reboot starting the cycle all over again. Then Neo has to select 14 men and 7 women from the matrix to escape and rebuild Zion after the machines destroy it and its current inhabitants. Or he can go through door #2 and destroy the matrix and everyone plugged into it, thereby destorying humankind. This has happened six times. The machines terminate those that escaped, the One looses his powers and those powers return to the source code and it all happens all over again. Killing, rebuilding, destroying, over and over again. This is the only problem but considering the alternative of death for the machines they are willing to accept it.
Considering all of this, the WTS is nothing like the matrix. They do not want to live in harmony with ANYTHING! They only take take take and don't want to give anything in return. Even though the matrix keeps you in a dream world it's a regular life for everybody and they don't limit you in any way. You can live any kind of life you want to in the matrix! It's more of a freedom than the WTS allows!
Edited to correct some errors in the plot.