I don't like it when ships have to tender but it is a fact of cruising life - especially when Mother Nature destroys docks. It does take some time and patience but nothing earth shattering. I have found if you wait for an hour or so after the first tender leaves and you come back to the ship about an hour and a half before she sails out you miss the long lines and crowds. I love Cozumel and every time I go there it's fun to see the changes/progress they are making. It has really grown up and changed in the past 15 years.
I wouldn't let the fact that you have to tender determine whether or not you get off the ship. If you think you might be interested in what Cozumel has to offer; go take a look.