Skunk Ape and the Florida Black Bear
Although their numbers have waned in the face of human encroachment, the Florida Black Bear can still be found throughout Florida and the southern portions of Alabama, Georgia, and Mississippi. They live mostly in protected areas, such as Ocala National Forest, Big Cypress National Preserve, Everglades National Park, Apalachicola National Forest, Osceola National Forest, and Okefenokee National Wildlife Refuge; all likely places for a skunk ape sighting, making misidentified black bears a popular explanation. Incursion by humans has significantly threatened their habitat, and the proximity of civilization has made run-ins between bears and humans not infrequent; which leads some to believe that the increase in interactions between human and bear could result in more instances of them being misidentified.
There is room for doubt in this explanation for skunk ape sightings. The first is the Florida Black Bear's size--they're relatively small for bears, with males averaging just 300 pounds. And while skunk apes are reportedly smaller than their northern cryptid cousins, they are commonly depicted as being taller than the four to six foot range that these bears average in length. Many sightings of skunk apes are of them in motion, too, and eyewitness descriptions mention specifically that they move bipedally--something that bears generally don't do. It seems unlikely that someone would confuse a quadrupedal bear for a bipedal hominid under most conditions. Certainly, if all that is seen is a quick glimpse of something large and dark in a heavily wooded area, then the chance of misidentifying a bear exists, but many of the strongest reports to come out of the south involve a much clearer view of the creature; such as Richard Smith's 1974 sighting. The odds of Smith, another civilian eyewitness, and a police officer all mistaking a black bear for an upright walking hominid is slim. So, if you're looking for a convenient theory to explain away skunk ape sightings, then you'll have to look further than the Florida Black Bear.