The book concludes the same way, with the train, rusty and dirty, finally being allowed out of the tunnel. The tenor is very much that punishment has rendered him meek and docile -- nothing to do with confronting your problems.

Similarly, there's a story where one of the trains gets off the tracks in order to smell flowers, or play, or something of that sort. The cure is to hide people in the field, who jump out and scare him back onto the track.

Overall, the message of the books is that if you work hard and never question authority, you can avoid punishment. The odd thing about them is that the authority figure (the Fat Controller) is presented as mildly risible.

My brother and I used to laugh / shudder at how much our nephews loved these books. I myself never read them until uncle-hood, when I was well past the age when the mere fact that they were written about trains had any appeal.