For most southerners, the Civil War was an existential struggle for the preservation of the only lives they knew, which unfortunately were intimately tied to the welfare and fate of thousands of slaves, who provided the cheap labor that kept the South's plantation economy alive. In fact, the establisment of the Confederacy under President Jefferson Davis and the move to secede from the union was grounded in these concerns about the southern states' ability to preserve their way of life and to resist the imposition of dictates from the wealthier states north of the Mason-Dixon Line.
The issue of states' rights that stood at the center of the Confederacy and, thus, at the core of the movement towards a civil war, was intricately interwoven with the issue of slavery, which was the most visible and economically vital issue for the South. Abolishinists, and there were some in the South, posed a clear threat to southerner's way of life, and, as with many peoples the world over and throughout history, many of them were willing to fight and die to preserve that way of life.
The Civil War's aftermath, characterized by the era of Reconstruction, was further proof among the now-defeated southerners that their brethren to the north harbored hostile designs for the American South. The series of laws passed by Congress, known as the Reconstruction Acts, prefaced with a reference to "an act to provide for the more efficient government of the Rebel States," would remain a cause of hostility for southerners for years to come. Implementation of Reconstruction included establishment of military districts across the South to be administered by Northern generals. As noted in documents from the period produced in accordance with the military orders involved, military occupation was imposed "due primarily to the fact that the introduction of Negro suffrage was thought to be possible only through a show of strength." [War Department Records, National Archives and Records Administration]
In short, the causes, conduct and outcome of the American Civil War were directly linked to southern hostility towards northern dictates, and vestiges of that hostility would remain for another hundred years, or more.