I assume you’re referring to the battle flag of North Virginia (dark blue square version) which was later also used by the Army of Tennessee?
There’s no harm in it. For most it represents Southern pride and heritage, although some actually used it, and still do, as some kind of backhanded racist sentiment. Most people don’t even know that it wasn’t the real flag of the Confederacy, but rather something popularized later in the 20th Century.
Whenever I see it on the back of pick-up trucks, on t-shirts, or even proudly hoisted on a pole, I don’t see anything wrong with it and don’t see it as something racially charged. I, on the hand, prefer the American flag.