You assume incorrectly. I have do have a problem with the Confederate flag being displayed. It's a symbol of treasonous stubborn immoral defense anti-black race-based inter-generational slavery. I also have problems with the Nazi flag being displayed. It's a symbol of racism and antisemitism. 

The American flag on the other hand is a symbol of a nation that always seeks to be perfected. Not a perfect nation, not an "exceptional" nation, but one that strives to move forward. A nation that strives toward liberty and justice for all, not just some. Protest is one means of perfecting the nation. Mindless allegiance to the status quo doesn't result in positive change.

The one silver lining with seeing the racist Confederate flag is that it lays bare the racist inner mind of the Confederate flag waver. It's pretty telling what kind of person would still pledge allegiance to the racist anti-black Confederate flag in 2017.