You used to have to farm up this whole separate magical currency to use aetherytes because teleportation wasn't an easy thing. Now, after the calamity, the land is so saturated with aether that the old currency was no longer needed to make teleportation work. However the damage to the city-states was so great following bahamut's rampage, that they have decided to charge a teleportation tax to help with their rebuilding, and the cost is calculated based on proximity.

That's the lore explanation of it, anyhow.