This was written around 1903 if memory serves me right. Back then, there was probably still a lot of bitterness over how the constitutional rights of the South had been ignored by the Union in the Civil War. And there is still today, even. :D
My guess is this song is directed towards two types of Yankees - neocons who from the start were the ones who rejected their right to independence, and those Yankees who think that the South is just a bunch of inbred redneck racists.