Hollywood Economics Trumps Truth
I think that up until the fifties, the common perception among movie producers was that an unsympathetic portrayal of the Southern cause would cause resentment and boycotts among Southern movie-goers, whereas Northerners would be more likely to overlook a sympathetic portrayal of the Southern cause.
(People on the wrong side of an argument are usually the ones most intolerant of opposing views.)
Hence the many Civil War era films told from a Southern perspective: "Birth of a Nation", "The General", "Gone With the Wind", "Santa Fe Trail", to name a few.
If you want to maximize revenue from your Civil War era film, tell the story from the Southern perspective, or at least feign sympathy for the Southern cause.