You won't fly to Hol Chan, which is a Marine Reserve, but to one of the two cayes near it, Ambergris Caye (aka San Pedro) and Caye Caulker. Either way you'll need to make special arrangements up front with a dive center, as you'll arrive after the boats have left for their first morning dives. Given that planes leave from the Belize City Municipal airstrip every hour on the half hour (approximately) and you can expect a 15 minute taxi ride to that airstrip from where you disembark the tender that brings you from the cruise ship, you'll need to work out which of those planes you're likely to catch. Then allow 20 minutes for the flight to either island, plus say 15 minutes to get to your chosen dive center (by taxi).
Having done all that, you may find you're in time for the first dive if the boat can be held back a few minutes, or that may be a lost cause and you will be able to get the second (boats normally return to dock between dives, though not always). The second dive leaves anywhere between c. 10:30 and 11:15.
You may well be able to do another dive after that second dive (which will be your first), but don't be surprised if you have to fit in with a schedule designed for other divers. You may have to have lunch before your second dive, which may go out anywhere between 1pm and 2pm.
You need up front to be sure you leave enough time to catch the last tender back to your ship, remembering that the cruise ship operators don't like people "doing their own thing" because they don't make anything from it, and they may insist that the last tender you're allowed to catch is not actually the final one. Decide which plane from San Pedro you'll need to catch (on the hour) and MAKE SURE you're on it.
If you decide to go to Caye Caulker all the above still applies, but remember that this is a request stop for planes and you must pre-arrange your departure with the airline. Otherwise the plane simply won't land. Doesn't apply to San Pedro as that is a terminus.
One more thing about Caye Caulker. Most dive sites there are further away than the SP sites, so the boats often don't return to dock after the first dive. So CC may not actually be a viable option for you.
Make sure the logistics can work and ensure you don't "miss the boat", then you can have a great and relaxing time. As to Hol Chan, it's fine if you're an inexperienced diver or have snorkellers with you, but if you're an enthusiastic diver I'd elect for two dives outside the reef off San Pedro. You probably won't have a free choice if there are other divers on board, but if you do I'd opt for Tackle Box as the first (great swim throughs at around 80ft, and a beautiful dive site) and Esmeralda for the second (usually masses of nurse sharks playing around you).
Write back if you want further advice/info.
I know the cruise ships offer several options in Belize. Just my 2 cents.
