Also know that the KKK are up North too - in fact, according to the FBI, OHio is the Number 2 ranked state for Klan activities!
The Museum of the Confederacy had an exhibit some years ago on the modern meanings of the "Confederate" flag (there were many more than one used in the Civil War - see www.confederateflags.org), and this exhibit inspired museum historian John Coski to write the book that Gerald cited already.
This exhibit showed a news film of the KKK marching in Washington, DC - thousands of them - and they were flying flags by the dozens - US flags and Christian flags. Not one Confederate flag could be seen in the film the entire time it was shown!
Hate groups have stolen many symbols over history and the Confederate flag is one of those symbols stolen (in the late 1940's). Yet the Confederate flag also has the meaning of resistance to tyranny for many. When the Baltic States of Latvia, Estonia and Lithuania seceded from the Soviet Union not long ago, you could see pictures of their people filling the streets - and some of them had Confederate flags! They were rebelling against Communist tyranny and used a symbol of rebellion to show it.
Americans today like things nice and neat, in a box, gift-wrapped and a bow on top. History cannot be put that way as it is far too complex and many events emant diffrerent things to different folks while they were happening. This is why you do research - to find out, as best you can - what happened and you listen to ALL of the stories involved. Most modern Americans don't want to bother doing that - but then they miss the truth.
Do some serious research and find out for your self. There's lots of sources out there to work with.