It's true that Cozumel isn't known for it's shore diving, to really know what Cozumel diving is all about, you need to get out on the reefs...and that means a boat ride.
Almost any dive op or hotel with a dive op on the island will give you unlimited shore diving if you are also doing boat dives with them, it is pretty much island wide policy.
"Dive with Martin" has some of the best prices on the island. "Blue Angel Resort" with their hotel/dive packages are very comperable. These are 2 that I have and still use and can highly recommend.
Having said that, there is some nice shore diving to be found on Coz. Sure, you won't get any of the awe inspiring coral formations you will out on the deep reefs & walls, but if you are a treasure hunter and don't mind poking your nose around small coral heads and rock scatterings, there is a lot to be found out there in the shallows. Just find a coral head and stop, spend 5 minutes or more being still around it, you will be amazed at what you find. You will find mostly juvinile versions of the same critters you find in the deeper water.
Generally the best shore diving is from the International Pier, moving north to just before you get to town. (or if you prefer from just south of town, south to the I.P.)
Basically anywhere from El Cid La Ceiba resort up to the Cozumel Princess. The middle area of that stretch is called Villablanca Shallows and before Wilma passed through, it was a beautiful garden shore dive, now in recovery mode is starting to come back very nicely.
This shallow stretch is also some of your best bets for finding sea horses, particularly around the Scuba Club.