It's hardly unusual for entities that receive government money to also charge for products/services produced using that money. Three examples I can think of just off the top of my head include 1) the health service in places like France where there are subsidised usage fees, 2) farmers in the EU who get large subsidies from the CAP or the equivalent in the USA, 3) application fees in patent offices.

It is definitely super annoying that this data is not free, but the reality is that it does cost a bit of money to gather and aggregate.

Furthermore, though I frequently take the train, I do consider it unfair that general taxation revenues are used to fund the train services -- especially considering that if you look at the stats they are principally used by the wealthy. Charging for data goes some way to shifting the cost burden of rail back onto the rail travellers themselves, as the person ultimately paying for this data is the traveller that uses the train time app/website.