I have no doubt that some, for generations, have used the Confederate flag as a symbol of resistance to integration or the civil rights movement, but my own experiences, my own observations, and the views I've heard from most people I've known throughout my life - black or white - was that until the past couple of decades the flag wasn't symbolic of any such thing for them. They saw it as nothing more than a piece of cultural history symbolic of a region... no more, no less.
The pics of the Clinton/Gore campaign in 92 using the flag illustrates this well. They certainly weren't using it to offend anyone and surely wouldn't have used it if they thought of it as offensive or representing any of the negative things it does now.
The current outrage over the Confederate flag is a bit artificial and mostly a recent phenomenon. It's also a case of selective application of what to decry or condemn. Is the American flag from the 1700's any less symbolic of slavery? It was the flag that flew over a country where slavery was legal in virtually every area and the law of the land. What about the state flags of New York or Pennsylvania? Although slavery was in the process of being abolished, it was very common once and wasn't actually outlawed and ended in those two states until 1827 and 1847 respectively, and was still legal throughout most Northern states until the late 1700's to early 1800's. Do we insist that those states take down their flags because they once supported slavery? Notre Dame once refused admission to Blacks. Does that make wearing an ND jersey symbolic of that and taint all of ND's history beyond repair?
The answer, of course, is no for several reasons. First, slavery and discrimination were never the only things those states or ND or our nation were about. Also, times were simply different then: the entire thing was seen in a very different light at the time and those people were products of their time just as we are of ours. Last but not least, people, cultures, schools, churches, states, and nations all make mistakes, all have some not-so-good moments in their past, but hopefully learn from those things and change for the better. George Wallace attempted to block James Hood from enrolling at Bama in 1963. Years later the two would become good friends, Wallace would repent of his segregationist stance, and be re-elected governor in 1982 with 85% of the Black vote. Our nation changed its views on slavery, renounced its past mistakes, and moved forward.
Don't throw the baby out with the bath water. Every state, school, church, person, and our nation itself has parts of its past that aren't perfect. Those things don't necessarily define them forever or override the good things they did or stood for.