Displaying the flag offended some shoppers, but not everyone, WJXT-TV, Jacksonville, Fla., reported.
"To me personally, I think it's disrespectful, I know southerners got their own beliefs, white or black, but I don't like the Confederate flag at all," shopper Richard Bradley said Wednesday.
Another shopper saw it as the use of free speech.
"I feel like it's your free speech, whatever you want to do," shopper David Grimes told the TV news.
However, in a statement sent to the television station, Winn Dixie spokesman Robin Miller said: "This issue was an error in judgment and has been corrected."