I notice online purchase for a rafina-naxos ferry ticket adds a 6.88 Eu "service fee." If you purchase the ticket at the port, does this same charge apply?
You must have made the mistake of using a third party website like ferries.gr which charges extra fees.
To buy your ferry tickets go directly to the ferry company's website.
For Rafina → Naxos it's probably either Fast Ferries or Seajets.
https://fastferries.com.gr/en/
You take an e-ticket and have it on your smartphone (or print it out).
Also note that in general it is useless to book in advance if you are there 1 or 2 days before departure. You can buy your tickets at a local ticket office at the port even on the day of departure.
Ticket offices at the port charge around €1 per ticket.