You’re right, having to do the fueling yourselve on each train is way too much work indeed and would only be tedious and should be done automatically. But having to take into consideration fuel prices, engine efficiency and track length when choosing which locomotive you’re going to use and wether or not it will make refueling stops along the way I think would be pretty cool.
On the business side of things, there are a lot of interesting things you could do with the pricing. How about investing in an oil company in return for discount? How about if you start to grow really big and use lots of fuel, prices go up? How about global things affecting prices like riots in oil producing countries or eco disasters and such.
If the price would be fluctuating a lot maybe think about storing it, buying it when it’s low and storing it to run your trains cheap for a while. There’s a lot that could be done and with fuel in the game 🙂