The shortest answer is that if they didn't there would be no plot. The slightly more in world answer would be that the machines are a life support system for human culture, not just our bodies. If the world was being terraformed back to habitable status over the course of thousands and thousands of years you couldn't just keep people living in hellholes like Zion the whole time, the matrix becomes a bottle garden of what culture used to be like to seed back into the world once there's a world for us to go back to wrecking. Again, just like Wall-E, really! If you just regrow people from seed-stock once the world was reborn they might accidentally grow up to be dirty tree hugging communists after all.