Ok, so can you understand the anger of Blacks toward that flag your ancestors fought under? Had your ancestors won that war, the Blacks would have remained slaves. I realize the war wasn't about keeping slaves in bondage, but the fact remains, had your ancestors won the war the slaves would have remained slaves.
The slaves probably would not have remained slaves, because in the Southern cities, agitation was growing due to immigrant laborers who resented the fact that they had to compete with slave labor for work. Political pressure from the cities (particularly the seaports) would have forced slavery to end by the 1870s, had the South won.
You do know that there were Blacks who fought under that banner as well. There's even a society for descendants of Black Confederates. They aren't angry toward that flag.
That was the battle flag anyway. The formal national flag of the Confederate States of America was different. The Naval ensign was similar to the battle flag, and in fact the flags that are sometimes seen today are more like that navel ensign than the square Battle Flag that the Army of Norther Virginia (among others) fought under.
This was the first national flag of the Confederacy:
http://www.confederateflags.org/images/SBVicks.gif
This was the second, which as you can see did incorporate the battle flag motif.
And this was the final one
(In searching for the information at that first link, I found this on, on Lee's "body servant", Rev. William Mack Lee who had been a preacher before the war started. He had been a slave on Lee's family lands, but all Lee's slaves were freed 10 years before the war began. He was still alive in 1918, with eight daughters ,twenty-one grand children and eight great-grand children, as of that year. It's an interesting little vignette.