I think the problem with commuting as exercise is that it is too routine. Clearly, it is better than no exercise at all, but the returns in fitness start to decline with the exact same level of exertion each day. You will eventually reach a plateau and just stay there. If you change your exertion level each day, I think you will find improvement, just as a farmer does when they rotate the planting of their crops. One day a week try to ride double the distance and another to ride hills, speed intervals or head winds to get your heart rate up.