I was there in April - before the swine flu (or whatever the PC name is for it). That was my third time in Cozumel. Never had any problems. I felt safe.
I was on the first ship back to Cozumel after the swine flu panic. No problems except the streets were empty and the vendors were dying for business. The locals said the epidemic never actually hit their island, was only on the mainland.
Sounds like you already found something excited to do. Swimming with the dolphins should be a lot of fun. If you go shopping make sure you get a cab to downtown as that's where they say all the 'deals' are.
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