drl:
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.
Cozumel is not on the malaria list as Dr. jpomerantz confirmed. Before I moved here, I went to the travel clinic in Austin and got all necessary vaccinations, updated my tetanus and got my hepatitis vaccinations. They gave me malaria pills just in case I was traveling outside of Cozumel/Cancun area (ie: Belize, south American, etc.), but NOT to use in Cozumel.
There have been some cases of Dengue fever here, but not epidemic cases.
Interestingly enough, the week after Emily, one of the doctors from the Mexican equivalent of the CDC was here in Cozumel to assess the mosquito situation after the hurricane. I had the pleasure of speaking to him and his wife (also a Dr.) and was pleased to learn what they are doing to improve the mosquito problem and to prevent epidemic cases of Dengue fever and other mosquito borne diseases.
Trucks spray every night throughout the island (with a new chemical that is not harmful to man or animal) and is quite effective for the mosquitoes. In addition to this, they have placed numerous magnetic type devices all over the island that each covers up to 5 acres. This is an experimental thing they are trying...so we don't know if they actually work yet.
In October 2001, I was diagnosed with a very mild case of dengue (like a REALLY bad flu), so I was very interested to hear of all of this. They also explained to me that the hemorrhagic dengue fever is very rare, and only occurs if you get dengue a second time and it is a different string of dengue. A single dengue virus is not hemorrhagic, it is when your body carries two strings and they counteract each other to produce the very dangerous hybrid of the virus combination. However, they have only seen one string of Dengue here, so that was very positive news for me  This is how I understood it anyway.
Point is, you shouldnt need any shots that you shouldnt have even living in the USA. My best advice for staying healthy while vacationng in Coz is:
1. Be prudent but not overly paranoid about what/where you eat
2. Stay well hydrated with water (all water served is bottled water as is ice)
3. Dont overindulge on the alcohol
4. Wear plenty of sunscreen (biodegradable please)
5. Have fun!!!!