Some groups use the Southern Cross as one of the symbols associated with their organizations, including racist groups such as the Neo-Nazis and the Ku Klux Klan.^[22] The flag is also sometimes used by separatist organizations such as the Aryan Nations. The Aryan Nation also uses the U.S. flag as well as the Christian flag displayed in some Protestant churches.

Supporters of the flag view it as a symbol of southern heritage and the independence of the distinct cultural tradition of the South from Northern government. Due to its ban in some schools and universities that have viewed it as a racist symbol, display of the flag has, in these contexts, also been considered an exercise of free speech.^[23]