@nuke: Well Fernandina Beach could be nice. It's close enough to Jacksonville to scavenge, if you're willing to brave the hazards there. The only problem is narratively the area is known to be abandoned and empty of any life, so your faction background should take that into consideration. If I may make a suggestion, why not run aground a cruise ship and make your faction one that has sailed around aimlessly for 200 years and now with the ship falling apart, you have to make landfall. It would explain why you have casino facilities and be a good foundation for any larger sort of factional idea. Also, you would be able to pretty much pick anywhere on the coast you'd like to start, regardless of the area's history.
The main warning here, is regardless of where you start, if the area is "known" you'll have to incorporate into your background where your faction came from or why no one's noticed you for 200+ years. For reference, most of Florida and Georgia has been explored and scouted and qualifies as "known."
If you're set on the Jacksonville area, Fernandina Beach is probably the winner for you. It's a RL resort kind of area, and actually bears a remarkable resemblance in some places to the Point Lookout DLC in Fallout 3. Gulfport and Biloxi could be good picks if you wanted somewhere unexplored and closer to New Orleans.