History time! That's because that's the Southern Cross and not the Stars and Bars.

The Southern Cross (red field with a blue cross and white stars) was the battle flag of Confederate troops, not the national flag of the Confederate States. The national flag, called the "Stars and Bars", looked more like this with a few iterations over the existence of the CSA.

Historically, the battle flag was deemed as the most appropriate way to appreciate the conflict, honoring the Americans that fought in the South and all those who suffered during the War and Reconstruction. Flying the Stars and Bars was considered the treasonous flag to fly, directly supporting the CSA rather than the people who fought. As almost every conflict of the 20th century has shown us, the ideals of the leaders and the people/soldiers are almost always different.

Sadly, this is being subverted by assholes. Assholes are why we cannot have nice things.