Most ships use PDC as a service call ... in other words, only passengers who have booked mainland shore tours through the ship will disembark here. This would include tours to Tulum, Coba or Chichen Itza, as well as to water parks like Xcaret and Xel-Ha.
Your ship should offer a diving excursion in Cozumel, but I'm not a diver so I have no experience with these excursions. Fury Catamarans offers a great sail/snorkel trip and many ships offer this tour or it can be booked individually.
On the mainland, we enjoyed both Tulum and Xel-Ha, which is a large natural aquarium for snorkeling. Chankanaab Park on Cozumel is a nice place to snorkel, but if you're a diver there are better reefs to explore, namely Palancar and Columbia.
I have found most ship's excursions to be worth the money, both for the quality and the convenience, but if you do a little advance research on your destination you can often book identical trips for 10-20% less cost.