So I went to college in South Carolina, and this is my take on it. I get that people are proud of their regional history, but it is undeniably racially insensitive. I lived in Charleston (which btw is the town where the civil war began) and around the town there were TONS of memorials to the confederate defenders of charleston, tons of confederate flags, statues of prominent slave owners, and nothing- literally nothing, memorializing the millions of enslaved Africans that were brought into our country through Charleston harbor.
The fact is- the civil war was about the right of states to perpetuate slavery for the economic gain of their wealthy constituents. The confederate flag is a symbol of that. And even though time has passed, people are really not getting any closer to confronting the less savory aspects of its history, so to people familiar with the way the flag is handled in the south it also kind of screams- 'willfully ignorany and unapologetic about it.'
My advice, Get the flag in the original yellow if 'don't tred on me' is a message you feel strongly about sending.