The idea is that early morning workouts are supposed to stimulate burning more stored body fat, since you are in a fasted state. This attempts to play on the fact that our bodies evolved to store fat for times of famine when we were hunter gatherer's. Assuming that at certain times your tribe would come upon a berry patch or kill a large animal and everyone would stuff themselves and then not find another batch of food for days, you needed to be able to store body fat when there was food available and use it to get through the times when food was not available. I don't know whether one could assume from that that this same principal works within the context of a day rather than over many days.
An interesting aside is that one of the theories as to why women stop menstrating when their body fat level drops below a certain level is that it was unlikely that a pregnancy would result in a healthy birth during a time of famine, so the body naturally shut down the reproductive system to prevent this.
Even if early morning workouts do work at first, I would guess that the body rapidly adapts to them and adjusts its daily biorythms to a workout at that time. I know when I first started working out in the early morning, I felt nauseus and light headed, but after a few months I adapted and now find I have as much energy on an early morning empty stomach as any other time of the day.