The confederate flag is allegedly a symbol of "southern pride". (Fun note: "pride" is one of the seven deadly sins.) The complaint is that people perceive the confederate flag as a sign of racism, when it's actually allegedly a symbol of southern "pride".
Since southern culture consists of more things than red rectangles and giant blue X's, there are many possibilities for symbols that could be chosen to represent the south.
Nobody is forcing you to use the one that's associated with slavery.