For road, government is providing the road and public pays for bus ticket, personal car, delivery services etc.

For rail, usually railway building is already covered by government. People only pay for the train. Upkeep is usually covered by all sorts of subsidies.

Where do you think your car registration fee, fuel tax and toll road fee go?

I don't believe it only gets paid from the revenue of taxes that are relevant to car usage. Probably a share of it is paid by what I pay in income taxes

Just like a part of taxes I pay get used for transit services I don't use :)