Hot take: the machines in the matrix were proletarian and the matrix itself was a humane solution to preserve humanity from its own genocidal, scorched earth solutions that rendered the Earth uninhabitable. It's also possible that the iterations of it (first a paradise that was rejected by humans as uncanny or unfulfilling, then a nightmare that was rejected as unreal and horrible, then a succession of "ok so what if it sucks a bit, but like a normal amount?" attempts) are layers that people filter through until they end up somewhere they're satisfied.