Ok, so can you understand the anger of Blacks toward that flag your ancestors fought under? 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.
You do know that there were Blacks who fought under that banner as well. Yes, I have heard that and the history is dubious at best. Aside from those who were either forced into it, or did servant type work as slaves for the Confederate army, I question the numbers. I don't doubt there were a few and no doubt they were offered their freedom for fighting alongside the south. The fact they could earn their freedom by fighting for the south should not be something any defender of the South should want to brag about. It begs the question of why they were in bondage in the first place. What is a more telling number is the huge number of slaves crossing over the union lines in order to gain their freedom. Any suggestion a slave fought for the South voluntarily because he wanted to be a slave is absurd. You know, the South lost the war and that is a very, very good thing. All these claims that the slaves were happy or that this war was not at it's core about the issue of slavery is simply an attempt by Southerners to justify something that can't be justified.