This is classic Stockholm syndrome with commutes that I see all too often.
What's wrong with the commute? The fact that, if you didn't have the commute, you could do all those same things and also anything else you can think of. The opportunity cost is enormous.
You can't have your PhD advisor at home, but consider how many people commute to jobs that could be done just as effectively from home/remotely. How many man-hours are lost to that.
Also, it seems like you're using public transport. You're lucky that that is a) a viable option and b) pleasant enough that you don't want to murder people after a few weeks of doing it. The majority of commuters around the world are using personal transport, which has a huge carbon cost and does not allow for doing other things while commuting.
Personally, I wouldn't mind a 40 minute train trip and a 5 minute walk either side, but a 40 minute drive is awful. I've gone from a 40 minute drive to a 10 minute drive, and I feel "free-er" because of it.
What's wrong with the commute? The fact that, if you didn't have the commute, you could do all those same things and also anything else you can think of. The opportunity cost is enormous.