There are two major reasons for this.
First, most white Southerners believed African Americans were inferior to them. Since they did not believe blacks were their equals, they did not see any reason to treat them well.
Second, African Americans were something of a symbol of the injustice that whites thought was being imposed on them in Reconstruction. They were being forced to undergo undemocratic rule, including military rule. This was largely (as they saw it) for the purpose of helping the African Americans. For this reason, the whites felt a great deal of resentment towards blacks.
Whites, then, saw blacks as inferior and felt the North was abusing the South for the sake of blacks. For this reason, they mistreated the African Americans.