For ship size of say a 10000 TEU container ship, fuel usage is around 100,000$ day.
For a 10 day trip 1M$. - 100$ per container fully loaded.
I don't see port fees approaching that value at all, would include the docking and wharfage fees - tug, security, berth space, servicing, pilotage, container fees, tonnage fee, etc,.. a list. Difficult to get an estimate here as it takes some digging and calculating for each port as they are all not the same.
Not sure even how much loading, unloading costs - assuming 100$ container on a general container. Extra expenses such as temperature control, storage, dangerous goods, etc, would be reflected in the client charge upfront so even if the ship pays, he has already charged that to the customer.
Rough guestimates.
Note that a ship that size cost around 100M$, so the company has to recoup that cost and the financing insurance, which works out to be around 40000$day - 400$ per container per 10 day trip - largest expense I think, which makes sense as a ship not moving is not making any money.
Then maintenance, labour, head office costs, non 100% loaded -- ?? - 100$ per container.
A 1000 mile trip for a container would have a customer charge in the vicinity of !000$, around a buck a mile.
Customer eventually pays for all the costs of shipping in his price to ship. A fully 100% ship makes more money per container.
Profit - If you add up those costs per container I get something like 600$ container, for a profit of 400$ per container on a 10 day trip - seems a bit excessive so I must be missing something in the guestimates - maybe 40$ per container per day profit for the owner is reasonable if one looks at it that way. Or $14M per year doing about 30 trips of 10 days each and 2 days at each dock.
That's the best I can do.
Some investigation would be in order to refine shipping costs.