The Animatrix (prequel) goes into further detail as to why the machines did it – it’s an act of mercy for their creators. They refused to fight humanity, and it was mankind who darkened the skies, in an attempt to disable the solar power that the machine race relied upon.
It’s not a prison, or some kind of torture device, or an experiment, but a way for humanity to continue living on a world that they made uninhabitable for themselves / incompatible with organic life.
Agent Smith : Did you know that the first Matrix was designed to be a perfect human world? Where none suffered, where everyone would be happy. It was a disaster. No one would accept the program. Entire crops were lost. Some believed we lacked the programming language to describe your perfect world. But I believe that, as a species, human beings define their reality through suffering and misery. The perfect world was a dream that your primitive cerebrum kept trying to wake up from. Which is why the Matrix was redesigned to this: the peak of your civilization. I say your civilization, because as soon as we started thinking for you it really became our civilization, which is of course what this is all about.