It has highly dubious and sinister connotations. It's associated with the southern states in America, and many extreme far-right conservative Americans use it as a symbol during their protests against equal rights for homosexuals, minorities and certain religious beliefs.
Symbolism is also highly subjective. The swastika for example is a symbol of good luck to some, and a representation of Brahma or eternity to others. Of course, when we see a swasticka however, we immediately think of Nazism. A flag is no different.