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What is today called "The Confederate Flag" or "The Confederate Battle Flag" is actually a combination of the colours of the Army of Northern Virginia battle flag with the design of the Second Confederate Navy Jack.
Despite it never having historically represented the CSA (Confederate States of America) as a nation, this 'flag' has become a widely recognized symbol of the South.

According to Civil War historian and native Southerner Shelby Foote, the flag traditionally represented the South's resistance to Northern political dominance.
The original (i.e. Civil War era) "resistance to Northern political dominance" was the same as the cause of the American Civil War - the southern states lack of faith in the United States government after sweeping victory of the Republican party, including the election of Abraham Lincoln as president.

More specifically, South Carolina, Mississippi, Georgia, and Texas each issued formal declarations of the causes of their secession, each of which identified the threat to slaveholders’ rights as either the dominant cause or a major cause of their secession.
The other seceding states also expreseed similar views.

During the Civil Rights Movement, the focal point of "resistance to Northern political dominance" was the fight against desegregation.

Since the issue of racial slavery was deeply intertwined with the causes of the formation of the CSA and since strong opposition to the Civil Rights Movement and strong support for continued segregation was primarily centered in the southern areas that were the CSA, it is difficult to not see the 'Confederate flag' as having some connotations of slavery and racism.

After the Battle of Okinawa a Confederate flag was raised over Shuri Castle by a soldier from the self-styled "Rebel Company" (Company A of the 5th Marine Regiment).
It was visible for miles and was taken down after three days on the orders of General Simon B. Buckner, Jr. (son of Confederate General Simon Buckner), who stated that it was inappropriate as "Americans from all over are involved in this battle".
It was replaced with the Stars and Stripes (i.e. the American flag).
Some comments from a couple some guys who should be considered most knoweldgable about the Confederate Flag and its origins/purpose.

Confederate States Vice President Alexander Stephens: The cornerstone of the CSA government would "rest upon the great truth that the negro is not equal to the white man; that slavery — subordination to the superior race — is his natural and normal condition. This, our new government, is the first, in the history of the world, based upon this great physical, philosophical, and moral truth."

Confederate States President Jefferson Davis: “From at least the time of the American Revolution, white southerners defined their liberty, in part, as the right to own slaves and to decide the fate of the institution without any outside interference.”

Confederate States President Jefferson Davis: The secession crisis had been created by the Republican Party's failure "to recognize our domestic institutions {a thinly veiled reference to slavery} which pre-existed the formation of the Union or {to recognize} property which was guarded by the Constitution."
by SouthBill54321 February 18, 2008
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