I use commuting as part of my training for racing: both base and intervals. Whether you develop fatigue or not will likely depend on how hard you push it. You will want to take some of the days at a recovery pace to avoid overtraining. If you can, you might also want to sprinkle in some total rest days. I'll typically take a shorter route, at recovery pace, after a harder day, and drive to work (using the car to bring clothes and food into the office) the day after a race.
On the diet. You are going to need something more than pure protein; specifically fat. Carbs tend to take care of themselves, but you need to focus to get a good ratio of fat and protein. During base phases, part of what you are doing is to train your body to use fat. You do that by keeping the intensity down in the "fat burning zones", but also by only giving your body fat to burn. Eating fatty proteins forces the development of the capacity to burn fat. The more fat you can burn, the longer you can go before fizzling out. You want to gradually increase the intensity at which you switch over from burning fat to burning carbs. The crossover point can be determined with metabolic testing. You want to push the crossover higher and higher. Your body has an endless supply of fat, but that is not true for Glycogen, and you can only replace the Glycogen at the rate of around 300 calories per hour. You can easily burn more than that, and so if you are relying on Glycogen, you are going to hit the wall.
On a morning commute of 25 miles, I would eat nothing before the ride, then have some fatty protein when I got to work. Nuts, avocado, good cheese, peanut butter, etc. I'd fuel the afternoon ride more, with an afternoon snack, then eat a normal dinner. During base training, for longer rides (3-6 hours) I fuel with peanut butter.
Diet needs periodization, just as training does.
My approach has made me, as our team physiologist said, "a model of metabolic efficiency". But then, my high intensity power sucks - I haven't spent as much time on that part, and getting the right balance is both science and art.