Yes. White supremacy was the norm then across the whole US, even in the north. That's not what we're discussing.
The flag was created as a symbol of a group with clearly-stated white supremacist ideals (see below), and flying it today at a courthouse is a constant reminder to many that some folks here still support those ideals.
Again, the founders of the confederacy meant to leave nothing for interpretation:
“Our new government is founded upon exactly the opposite idea; its foundations are laid, its corner-stone rests, upon the great truth that the negro is not equal to the white man; that slavery subordination to the superior race is his natural and normal condition. This, our new government, is the first, in the history of the world, based upon this great physical, philosophical, and moral truth.” - The “Corner Stone” Speech
Neither side was perfect in these times. But symbols of oppression still matter.
The least we can do is say we no longer support what this symbol stands for, and by flying it on our courthouse grounds, we're doing the opposite.