Boat day-trips from SP end up more efficient time-wise --- you are picked up at your hotel and dropped directly back at the end of the day. Yes, the flight is 20 minutes and the boat ride an hour, but you would have to go to town, check in for the flight, fly in, wait for the tour to get rolling ..... and will have to finish up the day on a rather tight schedule to meet your return flight. With the boat ride day-trip from SP you also get the experience of a wonderful jungle river ride. Lamanai is a long day but a spectacular ruin. Al Tun Ha is a very easy day, and also a wonderful spot.
For cave tubing - flying in makes sense - the logistics for that work very well.