"The Second Renaissance" in The Animatrix justifies it rather better.
However, honestly, what happened to humans in The Matrix universe is a kindness: humanity may not know the real world, but the people still get to live out their lives as if the apocalypse (of our own doing) had never happened. The machines could've given humanity hell, not:
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 misery and suffering. 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
However, honestly, what happened to humans in The Matrix universe is a kindness: humanity may not know the real world, but the people still get to live out their lives as if the apocalypse (of our own doing) had never happened. The machines could've given humanity hell, not: