Barbara,
In the same situation, this is the method I'd probably use.....
- Since you won't have to be on the Bus or touring at the appointed time as you have for the previous 12 days, treat yourself by sleeping in and then have a nice leisurely breakfast at the hotel. There will probably still be a few of the other tour members there to visit with.
- Your guide will work out post-tour transportation for all tour members. At the appropriate time for the flight departure time you've booked, check out of the hotel and take a Taxi to Napoli Centrale.
- Travel via Freccia high speed train to Roma Termini (1H:10M) and then the Leonardo Express to FCO (about 32M).
- Use one of the budget airlines to Prague. Regarding the airlines.....
I only checked briefly, but I don't know if there are any direct flights from Naples to Prague. If you don't mind longer flights and a layover, then you could certainly fly from Naples. Rome is a larger airport and has a greater choice of flights. Although not all flights for Sept. 2015 are listed yet, you could check Easyjet as they have direct FCO - PRG flights (1H:55M). You may have to use an early evening flight unless you don't mind a very early trip from Naples. There are several other budget airlines (ie: Wizz Air, Vueling) that offer flights from FCO, but I'm not sure if all of them offer flights every day.
The South Italy tour is awesome, and I'm sure you'll have a wonderful time.