The way of the Train Man.

Of course, Elly cannot, despite her clear wish otherwise, exist in isolation in a happy void in which she doesn't have people make cruel, insane and hateful demands on her time (and, no, her mother isn't right about how she'd go stir-crazy in a minute if she actually WERE on her own.) She, like all of us, exists as part of a family. The interesting thing is that in a very real sense, her lack of interest in the question "Why is this person doing this?" leads us to a rather unsettling destination:

Axiom 2a:

1) In every way that matters, Elly doesn't know much more about what makes John tick than she did when she found a nerdy dental student asleep in HER chair forty-seven years ago.
2) The same applies to John himself.

Since the strip is mostly about how it took until the Settlepocalypse for Elly to realize that her life has always been pretty good, we don't get a lot of back story on John. We usually experience him as Elly does: a baffling, huffy ogre who insults her, demeans her, makes light of her dreams and insists on his right to do so lest society collapse and his children be deprived of happiness and order. Certain facts, however, can't help but emerge. We have to deal with his constant nursing of his oh-so-easily wounded pride, his insistence that everyone else lighten up when he behaves like a jerk, his lack of friends and his need for ego-gratifying toys to make up for what he insists was a childhood of constant toil. We also have to deal with his being a dumb son-of-a-bitch when he's not in his surgery. This tells us two facts that Elly has yet to learn.

Axiom 2b:

Given his strident need to make everyone in sight live his idea of what a happy childhood should be, John seems to be driven by a feeling that his own past somehow failed to meet an artificial standard and he needs to have that fake injustice redressed.

and

Axiom 2c:

1) Outside a very narrow range of competence, John is a dullard who lacks common sense, awareness, wisdom and curiosity about the world. 
2) He uses the dangerous substitute called "folk wisdom" to compensate for lack of real knowledge.