A dark, painful period of American history that is still being felt and debated today... it's not something that should be celebrated.
No matter what people argue, it has been used as a symbol of racism for too long. People that want to flaunt that image, no matter how much they aregue about heritage, rights, or history... they are opening themselves up to criticism.
It's no different than a swastika.
You are aware that the swastika is a symbol that has been used since the begining of time in almost every culture.
Back to the confederate flag, it is an unfortunate fact that it has been and is associated with racism. While slavery was an important factor in the civil war, it wasn't the only one. From a purely constitutional point of view, they probably should have been allowed to leave.
While it is still a symbol strongly used by racist people (ie the swastika) it's not the sole reason why the symbology is used and exists.