I thought I would write an essay or something about semiotics and the confederate flag, then I googled it and saw it had been done like 50 times over.
Here's the first one: http://xroads.virginia.edu/~class/am483_97/projects/sarratt/intro.html
It seems like bad branding to use the confederate flag, a symbol that signifies hatred and racism, as a symbol of southern heritage - especially when that heritage is tied to a history of slavery and segregation. Saying that this is a small amount of people who understand the confederate flag this way (it's not) or that dissenters don't get it (we do) doesn't make up for the idea that this sign has always carried with it the ideas of supremacy, hatred, and disenfranchisement. These reads of this sign will probably not change, especially if we keep moving toward removing entrenched racism and biases from our society.
It is bad branding, unless they are ok with that connotation, then it is intentionally meant to hold onto and express the ideas that white people are superior to black people. At best people who claim this is a symbol of southern heritage are purposefully ignoring the idea that this flag symbolizes hatred. Your sign is flawed. Your philosophy is wrong.