i went to yoga class. they said "we practice yoga without shoes on". I said "I'm not taking off my shoes". end of discussion, and class was fine.
same thing for you. tell him you can do whatever workout he wants, but you are not giving up the commute. if he can't handle it, or keeps bringing it up, get a new trainer. nothing personal, it just didn't work out.
congrats on the progress you have made so far.