Originally Posted by The Lore Team
...
Why does it cost gil to use aetherytes?
Many aetheryte camps were destroyed during the Calamity, which necessitated their reconstruction. However, this came at great expense, and so teleportation fees must be collected to repay the as yet unpaid debt.
However, the
gil doesn’t just magically disappear from your purse! Though it's not shown in the game,
it's collected by the guards keeping watch of the aetherytes.
On a side note, guards posted by each city-state's aetheryte can tell you about aetherytes and teleportation magic. If you're interested, see what they have to say!