After the 7th Umbral Calamity, the aetheryte network of Eorzea was thrown out of wack. In order to fix it, Ul'dah paid the Sharlayans (not the Archons/Scions of the Seventh Dawn) to fix it. In order to pay the Sharlayans off, they basically put a tax on aetheryte usage. Outside of Eorzea, it seems aetherytes require some measure of upkeep and it's customary to pay the people doing that a fee.

Aethryte teleporting is instant. My explanation for what Cid says is that he's a Garlean and can't use teleportation so he never thinks of it. We're just humoring him.

The other thing we've never seen people do with teleportation is move large quantities of items. It seems that while moving your own aether is relatively easy, moving the aether of something else is much harder. So teleportation can never oh... replace the shipping business. In order to transport anything in bulk, it needs to use traditional methods.

The aetherytes of all the main hub cities are well guarded. Ul'dah, Kugane and Ishgard are the most obvious about it. There's also the fact that most people can't teleport in quick succession, so most people use it for an emergency and not for normal travel.