There are two big reasons muscle break-down can happen in relation to cardio. There are three heart rate zones that your body goes through when you exercise. Zone 1 is up to around 65% of your max heart rate. Zone 2 is around 65-85% of your max heart rate and Zone 3 is above 85% of your max heart rate. These zones help us determine where the body is getting it's fuel from. For instance, when exercising at 65% or less of your max heart rate, the body is getting it's 'energy' primarily from the break down of adipose tissue (stored fat). Let us not forget however, that even though the percentage of calories coming from stored fat is higher when doing low intensity exercise, the total number of calories burned from fat is greater with higher intensity exercise.
Zone 2 exercise, or 65-85% of your max heart rate, is when you can no longer talk comfortably and is moderately hard. The body's primary fuel source in this zone is carbohydrates which comes in the form of blood glucose and as stored glycogen in the muscles and liver. During prolonged exercise at this intensity, amino acids are then converted into glucose and used for energy. This is what you do not want because amino acids (protein) exist in your muscle fibers and you do not want them broken down.
Zone 3, above 85% of your max heart rate, primarily uses the Phosphagen system. The Phosphagen system is where the energy released from breaking down Creatine phosphate, found within muscle cells, is used to produce ATP (energy). It is extremely limited and can only sustain small bouts of all-out exertion but can regenerate during rest periods (high intensity interval training, 30 seconds all-out, 1 minute rest). This is one of the many reasons why high intensity interval training is favored because the primary fuel source is not amino acids which is basically your hard earned muscle being broken down. However, do HIIT for too long and your Phosphagen system can no longer keep up with the demand and you enter the same risks as Zone 2 training.
Now let's talk about the second reason I, and many other athletes, prefer short duration high intensity exercise over steady-state, zone 2 training. There are many hormonal responses to exercise but the main one of focus I want to touch on is the release of Cortisol. Cortisol, or 'The Stress Hormone', is released when the body is under too much stress either from too much exercise or inadequate regeneration. Prolonged levels of cortisol in the blood (like after an endurance event) has been linked to abdominal obesity, excessive protein breakdown, tissue wasting, and weakening of the immune system. It is a highly catabolic hormone, meaning 'muscle breakdown', which is why we want to stay clear of anything that is going to cause excessive secretion of it.
To put it simply, we want to build muscle to lose fat because muscle burns more calories than fat and the more muscle we have the better our body composition and health is. We want to stay away from things that are going to break down our hard earned muscle because that can lead to a decrease in metabolism and a sure way to gain fat back.
So that is why you hear me talk about high intensity interval training and why I stay away from long, steady-state cardio, and why I don't overdo it.