I think you're pretty much right Hixee.
The top diagram is both simplified and wrong because it is assuming two flat surfaces are next to each other, when in fact it is rolling meaning that different rules will apply, as you have shown with the second diagram.
I don't know how much air resistance comes into it really. The nly time air resistance will make a difference is:
1. A really fat person sits at the front, causing a larger surface area for drag. In this case though, I'd imagine the weight of the fat person would go some way to cancelling out that added resistance.
2. One load of people is significantly heavier than another. Again though, I don't think this would really matter, because compared to the train itself, whose weight is in the tonnes, the people wont make enough difference for it to show hugely.
Of course, what I say applies only to coaster trains, and I admit the thing with the bikes has got me a bit. I have rambled on for too long now, and have probably made lots of mistakes, feel free to pick them out.
EDIT - Pokemanic, friction does depend on weight. It's calculated as "coefficient of friction X Normal reaction", and normal reaction is the weight of the object (mass X gravitational field strength). The heavier it is, the more friction it has.