It IS representative of history, but what history is that?
It's a history of demanding states rights at the cost of American unity. It's a history of believing that a "way of life" (euphamism for slavery) should be preserved, regardless of whether the prevailing (correct) view was that that way of life was detrimental to human beings. It's a history of racism, segregation, and rebellion against the federal government.
I live in the North, and my great grandfather was, I believe, in the KKK or some iteration thereof. Because it's my "history," which led me to where I am, does that mean I should brandish the KKK shield? Or allow my kids to dress up as knights for halloween? No. It may be part of my history, but it's not what you display from your flagpole, it's what you learn about.
Those who do so are adopting a message -- it's "we don't care what the federal government thinks, we're going to live our lives the way we want to under our beliefs." The symbol that they choose to use carries the connotation that those beliefs include segregation, slavery, racial inequality, and hate. It's a symbol that has meant (and continues to mean) a perverted form of "purity" and "separation." No wonder it's been adopted by so many hate groups.