I assume you're flying into the country at Belize International Airport? There are other ways to get here. Assuming that to be the case, most people prefer the speed and convenience of flying here direct from that same airport. The flight only takes around 20 minutes. Cheaper alternatives include boat as you've said, and also flying from the airstrip at Belize City Municipal. In both cases you'll have a taxi ride to Belize City, which will cost more than the saving if you're by yourself. I think the breakeven point is somewhere around three people. You'll also have considerable delay even if you fly from the Municipal, and great delay if you take a ferry. The ferries don't run very often, and there are several all leaving from different places - you'll have to know which to go to at any particular time. Don't rely on the taxi driver to tell you, as he's probably paid to take you to one in particular, even if it means you'll be waiting hours.
Most people choose the direct flight the second time around, even if they tried something else first time. There is also the point that if you pre-book your island hop they'll hold a plane for you even if your incoming international flight is horribly delayed. That's true of Tropic Air at any rate. I have taken off from the International Airport for San Pedro not far short of 9pm, when I had assumed that I would be looking for an hotel near the airport for that night. I have also been the only passenger on a plane that was put on just for me (again, with Tropic).