The Confederate Flag has been a subject of debate before the Charleston shooting.
It has been a symbol for racism for a lot of racist groups. However, a lot of people want to keep the flag as a point of pride -- they think changing the flag is tantamount to saying that they are guilty or ashamed of being from the South.
While they shouldn't have to be ashamed of being from a southern state, the flag no longer means what it meant in Civil War times because a few s***head racists ruined it for the rest of them. It's like the swastika, which also was not originally a malicious symbol but became one through the actions of a significant number of s***heads.
My own opinion: I think the timing of this, after the shooting, sends a mixed message. On one hand, it's implying that the shooter is not responsible for his actions because the flag somehow brainwashed him into doing it. Even if the flag didn't exist, it seems like he'd still be a troubled, violent scumbag. The flag has very little to do with why he shot innocent people in a church, but unfortunately, it is easier to change a flag than it is to fix all the more complex problems about mental health and inherent violence. Then they can say they "did something" to make the world less violent.
On the other hand, the flag was long overdue to be changed, and Charleston might just be trying to take a stand and say they will not accept this casual attitude towards fostering hatred between people.