Personally, I think the problem with this particular protest is exactly what you are saying.  That the reason they are protesting is completely lost in the rush to politicize it.  The right is screaming about disrespecting the flag, yet are the same group who defend the folks who want to fly the stars and bars, which is much more disrespectful to our nation and flag.  The left is screaming 1st Amendment.  Neither major political group is talking about why they are protesting.