do you mean you already have a shuttle bus through your trip but the meeting point is in the airport?
If this is the case, I can suggest few things:
1- get a hotel just next to the airport, use a regular taxi from-to airport to catch your shuttle. I would suggest Solymar ivory suites, its very clean, well priced, nice breakfast and 5 minutes from airport and can be booked over xpedia.
2- book a hotel and fix it with your operator to pick you up at the hotel not at the airport. The suggestion here is to pick your hotel location on their way (south from the airport not north) so that it would be easier they pick you up on their way (still the above mentioned hotel would be ok).
If this was not the case or you do not want to go through either options, you can try having your flight to marsa alam airport (RMF) it is 15 minutes off port ghalib. If not applicable your tour operator or your hotel should be able to help you rent a car or shuttle from your hotel directly to the boat
If you have a shuttle through your operator, it will be the same way to get back to hurghada (just to make sure, pay after you arrive, whether going or getting back, also keep the contacts of whoever helped you to rent the car/shuttle and the driver's contacts as well, tell them the date and time he should wait for you in port ghalib for the return, time should be couple of hours before your actual arrival, if your trip will end at 4 pm for example, tell him that he has to show on 1 1pm, and start calling over since 11 asking about his whereabouts and ensuring that he would be there in time).
hope this helps.