Charge what you want. While there are limits, passengers won't care as long as prices stay somewhat reasonable. Also they don't change behaviour according to price (or not yet, the dev tested it but it broke performance some time ago, hopefully at a later point it will happen). To get an idea just look what real train travel costs for a similar service.

The price vs. distance does affect happiness, but happiness does not affect anything at the moment as Mirko noted. I find the same price per km is actually a good approach to use for both shorter and longer services, perhaps high speed a bit higher.