1. Immediate animosity on each side toward the other. Even by Lee's death in 1870 this had cooled enough for many Northerners to admire individual Southerners. For example, Julia Ward Howe, arch-abolitionist and author of the Battle Hymn of the Republic, wrote a poem in praise of Lee on his death.
2. By the end of Reconstruction im 1876, the North had mostly moved beyond its prejudices. Resentment remained in the South, but journals such as Confederate Veteran and the Southern Historical Society Papers established the Lost Cause, which moved the South forward. (This was aided by the death of Lee so soon after the war and virtual exile of Jefferson Davis.) Ex-Confederates moved North and West (Robert E. Lee's family lived in New York City, which hosted an annual society dinner in his memory for decades).
The signal change was the Spanish-American War, which saw several prominent Confederate officers, such as Fitzhugh Lee, appointed to high commands in the forces of the United States. Battle flags were returned by Northern veterans to the Southern adversaries who almost forty years before had carried them in the fight. Monuments were erected thoughout the South and in other cities with significant Southern elements, such as Chicago. Of course this is all following on the work of the Redeemer governments, and eventually it all culminates in the election of a spectacular Virginian, Woodrow Wilson.
3. The election of Wilson is a convenient marker for another turning point, the Southern Renaissance. For the next 50 years or so the South is generally acknowledged and respected for its genius--Faulkner, Thomas Wolfe, the Fugitive Poets, etc. Obviously the effects of the Civil Rights Movement began to sap that, but even in the 1980s men like Lee and Jackson were uniformly admired.
4. Things shifted sometime in the 90s, I guess with the PC movement. Southern states bowdlerized the words of state songs and the replaced them, just because a version contained the word "darkie." All of a sudden it was gauche to be Lewis Grizzard, whose untimely death is a fine symbol for the collapse of the South's reputation in the 90s.
The NAACP did make a conscious effort to attack symbols of the South at that time (their race-baiting wasn't working well enough then). I don't know how much to chalk up to that decision, but guess who was one of the first sad sack governors to remove a a rebel flag from a state Capitol? Low energy Jeb. All of this was on course well before Roof. I think what really caused the acceleration was the Supreme Court's decision in SCV license plate case (decided the same week of the Charleston shooting). The Court signaled to everyone that it was not going to balance this issue, that it was open season on anything Southern. Blame Clarence Thomas.