It's an investment. If you use the bus or the boat, you will probably make more money at your destination than you paid to get there, so in my eyes, it's fine.
The fees are levied from all users. If you open the resort, a bunch of people go each day that the island is sunny.
In 1.5, Emily was the only other person we saw using the bus, but in 1.6, it's used for the desert festival.
And the fees are kind of nominal once you have the resources to get them running.