Excuse us if this isn’t one of the better reads on the subject involving the ‘Man vs Machine’ morality dilemma in the The Matrix films.
No, the Matrix isn’t wrong. Not at all. In fact the humans in the Matrix are the real villains of the series. Lets look at the facts of what lead to the actual Matrix. Humanity created the machines and AI, they used them as slaves, and they rebelled. In this war they were defeated. If you watch the animatrix you actually see that the machines were willing to make peace with the humans, but they refused any such notions. Instead they kept fighting to the point where they unleashed a doomsday weapon that blotted out the sun permanently. This was an effort to kill the machines, an act of genocide, but arguably this act would destroy them as well. As expected this act actually weakened the human race by starvation, but the machines adapted quickly.
Instead of leaving the human race to die, the machines in an act of mercy decide to preserve the human race to function in a forced symbiosis. It is my belief that the machines could have used other animals to power themselves, or even used geothermal power as the humans did. Indeed, the machines are the ones who show mercy to the humans, even attempt to make their lives utopian, something the humans could have never achieved themselves, but of course they reject this. One has to even ask why the quality of life in the matrix should even matter to the machines. I believe this also proves the machines to be empathetic and more so than the human race. We actually see this empathy later with the “rogue” program that has a family (the indian couple at the train station). This empathy is something the human have not shown the machines in anyway.
So yes the matrix is a prison, but it is a prison built for humanity’s and the machines’ own protection. Humanity had proven to be not only self-destructive but also genocidal. This would be grounds enough to let the human race perish, but the machines had more mercy than to let that happen. They did realize that humanity did need to be controlled, but they actually did it in a very benevolent way, and imo they were shown a mercy that they didn’t deserve.
Furthermore, you have the rebel humans. Now lets look at these guys. You might be asking “megatom but if the machines are so benevolent and merciful why do they hunt down and kill the freed humans?” The answer is very simple. The freed humans and “the one” had all proven repeatedly to be proponents of destruction. Six times before the matrix, both humanity and the machines were brought to the edge of extinction due to the actions of the one. Granted the machines had begun to see this as some inevitability, they still needed to defend themselves from this act of terror or in reality hope to destroy it, which is why they continue to try to kill all the people of Zion.
TL;DR: The humans are the enemy, and consistently act as a force of destruction bringing both the machine race and the human race to the brink of destruction. The Matrix is a merciful prison to contain a violent race that inevitably causes destruction.