The passengers thing isn't at all like Nuts & Bolts, really. It is a little annoying that you have to do everything "correctly", though -- they get mad if you get hit, don't blow your horn at signs, don't speed up/slow down at certain signs, brake by shifting to reverse (akin to braking a car by switching on the emergency brake, it's likely pretty bad for the train), and stop exactly at the right time at stations.
Basically it's like following the rules of the road except quite inane and useless since no one else besides evil trains are on the road.
Nevertheless, it adds for some slightly interesting side quests.
The Phantom controlling does, in fact, make for some interesting puzzles, too.