It sort of makes sense doesn't it? You get up early, then head off to the gym before breakfast and get in a good 45 to 60 minute workout on an empty stomach. And, as you've probably read elsewhere, you're supposed to burn more fat than if you had breakfast or a snack before you exercised. But does it matter?
The trouble is, this sort of reasoning is not all that useful. How much fat you store, and ultimately use, pretty much depends on your overall calorie intake and your energy expenditure, which is made up of physical activity and your metabolic rate over time. Overall, it evens out, so the main game is watching your energy intake (as food and drink) and energy expenditure in physical activity.
Think of it this way: there are 24 hours in a day and let's say you work out for an hour every day. The one hour of exercise is just one period in which you burn fat (and glucose). In fact, body fat is the main fuel when you're operating at low intensity like cruising around the house, or working in an office in between meals, or resting and sleeping. Except at very high exercise intensities, you will burn a combination of fat and glucose 24 hours a day. You still have around 23 hours to burn body fat outside of formal exercise time.
And here's what happens. Fat and glucose burning are part of a sliding scale. If you burn mostly glucose when you exercise -- as you might if you ate breakfast before hand -- then your blood glucose will drop and you will burn more fat after you stop. If you exercise on an empty stomach, then eat after, you will burn more fat when you exercise and less after refueling with a meal. You have to look at the energy ins and outs over a 24-hour period.
You can get into trouble exercising too hard on an empty stomach because low blood glucose and intense exercise can cause a lowering of your immune response -- and that means increased risk of infections and flus. My suggestion for early morning exercisers is to take a little carbohydrate in the form of a slice of toast and perhaps a coffee and sugar, or even a power bar on the run, within 30 minutes of your workout. If you're going to work out or run or cycle for longer than an hour, I would eat a little more, including some protein, and top up at the 75 minutes mark.
And if you're targeting weight loss in particular, make sure you don't overeat after the workout. This is a major issue for people who don't eat before morning exercise because the tendency to overeat is strong as a result of low blood glucose and increased appetite.
If you want to read more about fat burning, see my article: How to Burn More Fat.