I am just coming from the Keys. I am on a cross country tour, started in Philly last year in May and went in a circle around north america . Philly, Lake Michigan Connector, Seattle, San Francisco, New Orleans and then down the Gulf of Mexico Coast to Key West. (Took the ferry from Fort Myers to Key West and started there to go up the East Coast - Atlantic Trail ACA back to Philly)
I am now in Daytona and hope the weather will warm up while I am climbing up to the north.
On arriving in Florida I had the same worries like you. Saw the first gator in Central Florida beneath a bridge in brackish water, not moving. From that day on I had many gator sightings, but never felt endangered. there are also many signs on the road, warning from bears, panthers and gators crossing the road. The only bear I have seen was a dead one on the road shoulder, never saw a panther.
The Keys are simply beautiful and I wouldnt want to miss the experience. I stayed on campgrounds throughout the passage of the keys because Motels are very expensive. The campgrounds are very safe, most are fenced in and well kept. No danger there. The ride across the many bridges were for the most parts a pleasure. they are just building a bicycle trail from Key West to Homestead, some parts are still under construction.
There is one thing I would like to warn you about. I didnt use the aca route from Key Largo to Homestead on the 997 because it seemed a big detour for me. On asking at the visitor center in Key Largo I got the information, that riding on the Highway one would be fine, but half of the 1 is under road construction and a very dangerous ride. so better stick to the aca route.
wishing you a safe and enjoyable tourwww.on-bike.net
have a look inside here too http://www.conchrepubliccyclist.com/