Hi Gus,
I wouldn't let the risk of flu stop me. We have flu in LA too, so I'd rather be in Mexico. I honestly would be more concerned about flying at all, than the actual destination, but that would not stop me from going to Cozumel.
Cozumel is one of my favorite destinations, but at the same time I have to admit it can be miserable for photographers if you have certain expectations and dive with the wrong dive ops. If this is the first trip to Cozumel just about all the dive ops will keep a close watch on you for the first couple of days. When they see that you are a good diver they give you more latitude.
All the dive ops dive as a group, but some are much more strict than others when it comes to keeping the group together and following their lead. Others may take out even very small groups, especially now since business is slow you can probably find that pretty easily.
There are different kinds of dive boats there too. Big boats, small boats, fast boats, slow boats and cattle boats. You can't assume that all "fast boats" are a good thing or that all big boats are "cattle boats". Here is an article I wrote about that some time back when some of my friends asked about the boats: http://www.underwatercolors.com/Cozumel_dive_shops.html
For the meals your best bet is to go with a resort that offers breakfast and lunch, but allows you to be on your own for dinner. Especially if you're not staying close to town, you're going to want to have good food close by and fast just before and after diving. Down on the south end of the island there are not many choices. Even in town its really tough to find a cheap, good and fast place for breakfast. Scuba Club has a really nice 'light' plan that allows you to do this and their breakfasts and lunches are outstanding.
Airfares are REALLY cheap right now and there are a lot of summer packages. Scuba Club has specials that include rooms, diving, breakfast and lunch and you can do this easily for under $1500 including tips, etc. This time of year Cozumel is GORGEOUS!
Sorry if I sound biased about Scuba Club, but I've stayed at many different places in Cozumel and Scuba Club is one of the resorts I would always go back to in a heartbeat.
Depending on when you're planning to go, you're welcome to join my photo workshop in August. As far as Cozumel photography goes, you won't find better shooting opportunities than if you came diving with us for a week. SCC rolls out the red carpet for us and gives us much more flexibility as a photo group than I've ever gotten anywhere else. Here's some info... http://underwatercolours.com/cozumel_workshop.html. Maybe you can join us.
Bonnie