You're right that the Yucatan is considered a "malarial endemic area." But I know many people who dive there twice a year or more and no one has ever gotten sick (beyond the occasional Montezuma's revenge). The biggest effect is likely to be if you donate blood, since a visit to the Yucatan means you're deferred from donating for a year. Last I heard, this applies only to the mainland, not to Cozumel itself, but I'm no longer up on these things; since I lived in Europe during the 80s I'm permanently deferred due to the mad cow risk.
Mosquito repellent is definitely recommended if you go inland, but beyond that I wouldn't worry.