The flag is dear to some people's hearts because it is a battle flag of their ancestors... I do not share the sentiment for this particular flag, but I understand it. And you better understand it too -- for the healing to begin.
You clearly do not understand why some people in the south love the confederate flag.
It has nothing to do with history. It is a statement of identity - the identity of a "country boy." It's borne of a very deep inferiority complex. Rural folks see all kinds of great things on television that they will never have, because television is set in New York, L.A., and other cities. Rural economies cannot support the nice houses, cars, jobs, shopping malls, and priviledge they see, and they feel left behind.
These same people also feel very intimidated by things they don't understand, and they don't understand much.
So, the people who have confederate flag bumper stickers are not all racist. But, there is a strong feeling of resentment behind that flag, and some of that resentment does get directed through racist channels (just as Roof did).
This divide between rural folk and city folk is not unique to Southern United States. You see this conflict all over the world, frequently as rural inland dwellers v/s coastal city dwellers. It's universal.
So, no, the confederate flag has nothing to do with healing after the civil war or anything like that. It's a symbol of the red state/blue state divide. That's why you're sticking up for it, after all.