For many people, the Confederate battle flag is an attempt to distinguish between the heroism of the armies of the Confederacy and the evil cause for which those armies fought.
Fundamentally, the Civil War was about slavery. All you have to do is to a) read the Articles of Secession of the states, OR look at the nature of post-Reconstruction white rule in the states of the defeated Confederacy. (Or you could watch “Birth of a Nation” (dir. D.W. Griffith). See: https://www.youtube.com/watch?v=I3kmVgQHIEY Really remarkable.)
Slavery was an evil institution that showed no sign of evolving in a positive direction or dying out on its own. See: https://www.youtube.com/watch?v=n9JaQy6wfbE No, actually, the clip tells you all you need to know about slavery and the people who experienced it.
The armies of the Confederacy fought heroically and well against a stronger opponent. See: https://www.youtube.com/watch?v=R1Xu_Jni4V4 Often (although certainly not always), to be a native white Southerner today is to feel oneself to be an heir to this admirable legacy. There is nothing wrong with this sense of identity—unless there is also something wrong with “Band of Brothers.”
However, the armies of the Confederacy fought heroically for the freedom to maintain the racial supremacy of whites over blacks. (Not just slavery, when perhaps 1 in 4 Southern families owned a slave, but the legal and social superiority of any white person over any black person. See: https://www.youtube.com/watch?v=AbXTl0WX4RE.)
Curiously, Northerners fairly soon abandoned the myth of the victorious cause. Yes, for decades, Republicans politicians were prone to “wave the bloody shirt.” Yes, “Marching through Georgia” was played at the Republican national convention. (See: https://www.youtube.com/watch?v=xs43o85zot8.) However, the Spanish-American War (1898) is often seen by historians as a moment of national reconciliation. See: https://www.youtube.com/watch?v=RAYbLdpghRA Certainly, by the 20th Century, the Civil War had lost its power to inspire a sense of identity among Northerners. Today, one rarely sees a Prius with “Grand Army of Republic” bumper sticker or a Chevy Volt with an American flag license-plate holder.
In contrast, during the 1950s and 1960s, visible assertions of identification with the Confederacy in the form of the Confederate battle flag began to proliferate in parallel with the advance of the Civil Rights movement. For example, the Georgia state flag adopted in 1956—two years after “Brown versus Board of Education”–included the Stars and Bars for the first time. For example, the Confederate battle flag became a fixture at the South Carolina statehouse in 1962 in opposition to the civil rights movement.
It is not possible to disentangle the two strands of the Civil War in the South. It is not possible to claim only one part of the heritage of the South without claiming the other part. They were intertwined. There is no easy way out of this dilemma. All chortling aside, it is a dilemma which Northerners have never faced. So, it is a sense of triumph won without cost.
 In the same fashion, it is not possible to celebrate the triumph of the Westward Movement without acknowledging the chicanery, violence, and racism that robbed and butchered the Indians. My ancestors played a part in that and I am heir to its legacy.