Most non-Southerners see the confederate flag as a symbol of racism, no different than a swastika, and associate it with slavery and groups such as the KKK. Flying the confederate flag to honor fallen confederate soldiers insn't much different from flying a
WWII German flag with a swastika to honor fallen German soldiers. From what I saw when I lived in the South most, but not all, of the people who would display a confererate flag were pretty much racist rednecks. So, while I agree with some of your comments about the NAACP, I can not fault them for having a problem with the flag being flown over state property.

Symbols can be very powerful things and carry a lot of psychological weight. I am an athiest but would never desecrate a crucifix. I would not do this out of respect for what that symbol means to millions of people. I feel the same about flying a confederate, or nazi, flag. Whether or not the person displaying the flag is racist it is a racist symbol to millions so displaying is it in poor taste.