We love Captain Jacks and have been going there for years. The food is great (the clam chowder is the BEST clam chowder we've ever had anywhere). The crab cake melt is great as well, and I've always heard good things about the twin lobster tails.
The atmosphere is one of the most unique in Disney, there is a very nautical theme and you get to sit right on the water for most of the tables, very nice.
As with most restaurants, you're going to find people who hate them, and people who love them. People have a tendency to write more about places they hate, so I would give it a try if you're in the mood for some good seafood!
P.S. They also have some of the longest tenured bartenders in all of Disney, some of their bartenders have been working there for 20+ years!