Railroads are like a lot of other features in the game. If you've got a well planned nation with a strong economy then you can make reasoned judgements on whether you want them. If you've got unhappy people and no income then everything becomes an expense you can't afford.
It's needed for island maps. It's plain silly on pangea maps where you develop railroads and immediately replace your roads with ... ports. The whole roads/railroads system is pretty bad anyway. If roads are meant to be expensive then put in an up front cost for building them, scaling up as you go through the ages, and cut out the maintenance.
The harbor thing is in my opinion more of a bug than a feature. It's just ridiculous to give you a bonus for connecting your cities by railroad to your capital and all you ever need is to connect inland cities.
It's needed for island maps. It's plain silly on pangea maps where you develop railroads and immediately replace your roads with ... ports. The whole roads/railroads system is pretty bad anyway. If roads are meant to be expensive then put in an up front cost for building them, scaling up as you go through the ages, and cut out the maintenance.