Fred: There is a Farmacia right in the complex of shops adjoining the pier where most ships dock (some smaller shops dock right in town). This shopping centre includes the big duty free store and "Los Cinco Soles", Fat Tuesday's etc.
The Pharmacy is sort of in the middle of the complex, down one of the "cross streets". You'll find it.
I am sure there are other pharmacies in downtown San Miguel (Cozumel).
Stayed in Cozumel 4 days couple of summers ago. The mosquitos were extremely severe due to lots of unseasonal rain. I asked a taxi to take me to a Supermarket or Walmart (they're in Mexico too), can't remember which....but there was a "pharmacia" inside. Bought some industrial strength bug repellent that worked really well.
I believe I later saw a pharmacy in the center of town where all the shopping and restaurants are later on. Just ask a taxi driver to where the "pharmacia" is and it's about $4.00 per taxi ride anywhere in town. You can also get bactrim and other perscription drugs at the pharmacy without perscription.