Before, during and after the Civil War power struggles of all types led to widespread conflict. Bleeding Kansas saw Red Leg unionists leave a swath of destruction across Kansas and Missouri killing hundreds and causing thousands to flee smouldering ruins. Reconstruction was worse.
"White Caps" in New Mexico protested efforts by the government to fund public education, thereby replacing the church as the primary means of education. They would kill or torture government officials attempting to raise education funds. (They got their name because they dressed like the KKK.)
The list is long and ugly but it boils down to power struggles. Some were fighting to keep power, others were fighting to gain power. Many innocents were caught in the cross fire and most of these innocents simply wanted to be left alone. Doesn't work that way.