Ahh, actually I am mistaken. The white lightning and black panthers actually used the rebel flag, not the confederate flag. The official confederate flag was called the stars and bars, and looked different than the one you are referring to as the confederate flag.
The KKK also attempted to appropriate the rebel flag as their symbol, but were never as successful. This being the case, their attempts caused the black panther party to distance themselves from it, much to the detriment of the synthesis of civil right's protestors in the past.