the trip from Cancun to Cozumel was a pain in the butt. If you can fly into Cozumel, do it. To me, it is worth the extra $$. Quite a few people told me the trip would be easy, but I personally recommend against it (unless you have no other option). I think it wouldn't be as bad for me, now that I've done it and know what to expect, but it sure would have been nice to fly into Coz.
If you have to do it though, it is do-able. The day I travelled over it was in a terrible storm. The ferry ride caused many people to get sick (all over the boat), and if you take the bus, they will try and wait to fill the bus up (even though they'll tell you it will only be a few minutes). We waited in that bus for almost 45 minutes while they waited to make a few bucks, which I do understand but found it frustrating as it was getting very late.
All in all, it is better than not going to Coz at all though...