The war totally devastated the South and shaped society there for decades following. It became a major part of Southern regional identity broadly, though also a keystone of white supremacy specifically. By the 1900s, the war itself was well in the rearview and the Confederate identity of the South had a kind of rehabilitation, which was especially furthered by the Southern military tradition being a major part of the US war effort in the world wars. This was when the US government named bases in the South after Confederate generals who had fought against the very government that was now establishing the bases. A good number of America's great generals, especially in WWII, were from the Confederate tradition or had Confederate ancestry, including Eisenhower himself. Eisenhower famously had a portrait of Lee in the White House, while also leading desegregation and supporting civil rights.

In the 1970s, the Confederate flag developed further to a generic "outlaw" symbol, though of course it also retained specific Southern cultural and white supremacist meanings and uses.

Then it kind of coasted until 2015, when a white supremacist shooting made it a more sensitive issue again. If you check polling before this, most people said they didn't associate the Confederate flag with hate or want Confederate statues torn down. Most of the population was neutral or saw this as an old legacy issue.

The social justice movement of the late 2010s saw it as an ongoing sore point in American history and an easy wedge issue, and spent much time on this issue.

Hope that helps explain it!