Originally Posted by Lasereth

The machines know that humans are a powerful species. In order to keep them in-line, so to speak, the machines (or the architect to be precise) made the Matrix so the humans would think they're free. Killing all of the humans off is impossible. There will always be a resistance. Cows aren't capable of fighting the machines, so they were simply slaughtered. Humans are capable of the destruction of the machines, so the machines chose them as an energy source and put them in the Matrix to prevent a resistance.

-Lasereth