There are over 480 actual Winn-Dixie grocery stores scattered around the southern US. Maybe you've got a dog terrorizing one right now.
Neither Naomi nor Watley, Florida actually exists. Sorry, you can't go on a Because of Winn-Dixie neighborhood tour. Sigh.
(Google Map it. Not there…)
Bottle trees are a real thing. They were brought over to the U.S. by Central African captives, and now you can sidestep the whole alcoholism-and-ghosts thing and just buy a metal one to put in your garden. (source)
Dave Matthews played Otis in the movie version of the book. Hence, he actually did play the guitar. No stunt fingers needed here, thank you very much (source)