We have cruised to Cozumel on several occassions. Highly recommended is the shore excursion to Tulum, on the mainland. This is a long shore excursion (all day) that goes to the Mayan ruin site of Tulum, which is the only ruins that overlook the ocean. The views are trememdous and the ruins are very interesting. It is a shame that people go to the Western Caribbean and do not take advantage of the historical sightseeing of the ruins. Tulum is truly a site to behold and well worth the time and expense. By booking through a ship, you get door to door transportation and leave behind the worry of missing the ship. Also, the tour guide is very nice to have. Tulum is breathtakingly beautiful - bring a camera.
For a more beach oriented shore excursion on Cozumel proper, try helmet diving. It is available in the park (Chankanub). We especially enjoyed it as we could leave on our glasses and contacts and actually see things underwater. Also, it is a real hoot to walk around on the bottom with a helmet and breath normally. The park has a lot to do in it: great beach front restaurants with margaritas and nachos, snorkling (included with helmet diving), small ruins, dolphin encounter, etc.
Tulum runs around $85 for the shore excursion (ferry to/from Playa de Carmen to Cozumel where the ships typically dock or anchor), bus to Tulum, admissions, drinks on bus and box lunch), but be sure to buy the $1 ride to the ruins from the parking lot to avoid the long dusty walk.
helmet diving is approximately $70, inlcuding transportation to pier and back, park admission, helmet diving and snorkel gear for day. You pick when you want to return and can make it a full day.
Cozumel also has the Atlantis submarien ($109) which is quite a thrill to dive 100 + feet and shopping, bars, etc. There are some interesting artists on the square with very innovative (thumbnail paintings) that are very inexpensive.
Enjoy.