^^ I agree with this.
The machines did believe they were doing humans a favor by putting them into the Matrix. We see the story primarily as told by Morpheus, a major leader in the resistance who is very single minded on destroying the Matrix. But if the story were told from a different perspective, we would see that things are not black and white.
Even through a war machines fought with humans, the machines were still greatly benevolent in their intentions. Humans began to fear machines and came a point of wanting total annihilation of the machines, even to a point of ruining the world's atmosphere just to destroy them. Yet the machines never wanted to detroy humans, they still worked to come up with a resolution that would please everyone.
The machines recognized that by blotting out the sun, humans had ruined their own lives as well and many would be miserable living underground. The machines didn't turn to animals for battery power because they didn't care about them. They used people since they were still trying to live with their creators.
They understood them well enough to be able to re-create their world so people could be happy, and of course the machines benefit too. A solution for everyone. They made the first "world" utopian with this in mind, trying to provide an ideal humans were never able to achieve on their own. It was humans who didn't accept it. The current Matrix produced the best outcome, from the machines perspective, because it kept the highest percentage of people content.