I think the short trip thing is an exploit/bug.A few times I was picking up fish on a very short run and all the train ever did was switch directions as it picked up fish and dropped them off.. the train didn't even need to move just change directions..
All you need for a $1.5million dollar train is to connect two metropolises with maximum upgraded stations as close to each other as possible.
Then you make an 8 car train (4 mail 4 passenger), and it will flick back and forth all day picking up at least 1pass/1mail each time and making a fortune. Ideally you make it so short it only has to turn around.
If you add some steel or food to that train, then all the better. (Just build an industry in one of the metropolises if you need too)
This is the reason I only play randomised maps, as the good guys know which cities they can do this trick between , then go straight for it.
I think there should be considerable less money paid for passengers over such a short distance, and considerably more paid for passengers over long distances, to encourage longer, more realistic journeys.