The docking fee charged at a port is really only a factor to consider for new players. A player in a Marauder earns about 500 credits for a Dumont deliver, while a higher level player could easily earn 20,000 credits for a Dryden delivery. That represents 10% fee for a new player, and only a .25% fee for a high levle player.
In an effort to keep the Docking Fee a little more significant, I suggest to increase it based on the tier level of the ship. Perhaps double it for each additonal tier of your ship.
So a Marauder would pay a 50 credit docking fees, 100 credits for a tier 2 ship, 200 for a tier 3 ship, and 400 for one of the top level ships.