Here is my 2 cents
First off, I think you are probably working out plenty. Biking 40 km per day is a great workout and should burn plenty of calories. In addition, you work out other times, so the AMOUNT you are working out is no problem at all.
A good breakfast is extremely important in my opinion for feeling good throughout the day and also to even help your metabolism. It's always healthier to eat a little slower, and it sounds like you are really rushing your morning meal. I know it can be hard, but maybe wake up earlier or eat RIGHT when you wake up before doing other things. Doing a long bike on an undigested meal can leave you feeling queasy for hours from my experience.
Try to keep your eating consistent throughout the day. It's better to eat 2500 calories or whatever you eat per day over several meals and snacks rather than gulping down half in one meal. Your metabolism reacts quicker and better, allowing you to constantly store more energy and burn more energy.
Also, I've never been a huge fan of protein shakes. First off, if you do have protein shakes, make sure you're buying lean protein shakes with next to 0 fat. You would be surprised how many of the protein shakes have exorbitant amounts of fat and carbs in them. For some people, that's good, like football players and atheletes. This gives them more energy to burn and let's face it, most athletes, whether they are high school, college, or professions, burn MUCH MORE calories than an average person. This is why protein shakes are especially good for athletes. Not only do they get the protein, but also some fat (energy) to burn.
If you eat a healthy, normal diet, you should have plenty of protein to maintain your muscle. Muscle doesn't just evaporate. Honestly, muscle can dip quickly, but it's not really muscle mass you're losing. Losing actual muscle mass takes months of strictly not working out and eating a poor diet. The same goes for building muscle. It takes several months to actually build permanent muscle. If your protein shake has lots of calories, ditch it, or buy a leaner protein shake. You really don't need it to maintain muscle. As long as you continue to work out and have some protein in your diet, you'll be fine.
Finally, maybe you could try using a calorie counter? I find them actually really fun and entertaining. This will also help you guage your diet balance. Almost every person in America has way too much salt, way too much sugar, and not enough potassium. Challenge yourself to be well rounded in those categories.
My last litte bit is about eating after working out. Dont be worried it's going straight to fat!. You just worked out. Your body needs nourishment. It's healthy to eat a lot when you are done working out, so continue eating when you get home, just maybe eat slower and try and watch how many calories you put in. Avoid 1000+ at a time. Cheers.