Via the Accordion Guy: If the machines were really smart, they would have used Cows for their power source.
The only problem I could see that would cause them not to use cows would be if there were none. If humans really killed the sky, it would kill everything on Earth. Humans might have figured a way to grow somethings underground – what power source are they using? – but you wouldn’t keep cows around as they are inefficient sources of calories.