The answer is quite simple. Your body likes fat more than it likes muscle. Muscle is metabolically active and takes calories to maintain, whereas fat just sits there doing nothing. Our bodies are extremely efficient, and they try to maintain homeostasis if possible. All that muscle we have (or would like to have) isn't natural, per se, and your body doesn't like it because it burns too many calories.
Back in the day, we would feast for weeks and then fast for months. How did our body survive when there wasn't enough food? By storing fat when there was enough food, to keep us alive when we couldn't find any. Unfortunately, our bodies have not changed.
Try this... gain 20 lbs of muscle. Stop working out. After half a year, you will have lost a fair amount, if not all, of that muscle. On the other hand, your adipose tissue will probably have remained the same, or even grown.
When you do cardio on an empty stomach, your body will use both fat, muscle and any available carbohydrates. Since muscle is metabolically active tissue, and it's really doing nothing but putting extra stress on your body (as in, it needs more calories), your body will use it for energy. Muscle gives more energy than fat does, and ultimately, burning muscle will allow the body to go back to a state where it does not need as many calories to maintain anything more than the minimum amount it needs to exist.
So when you give the body some carbs and protein in the morning before cardio (just around 20-30g each), you'll save your muscle. In the end (assuming the right macronutrient ratios), as long as calories in=calories out, bodymass is maintained. So it doesn't matter whether you eat a bit before running... you'll burn those calories anyway if you keep a good diet.