He said he would never agree with someone disrespecting the flag. He didn't call them nasty names or say they should be shot (like some on USMB do), he just said he would never agree with them. That's it. The outrage over this is kinda stupid IMHO. I mean, there are lots of things that I will never agree with, and if asked, I will tell you what they are. But that doesn't mean I'm forcing anyone else to disagree or agree with me, I'm just expressing my opinion about something.
And, while I also won't agree with people burning or stomping on the flag, that doesn't mean I'm going to stop them or force them to quit. One of the things in the Constitution (which I swore an oath to support and defend several times while in the military) is the right to peaceful protest and free speech. If I see someone burning or stomping the flag, while I may use some choice words in expressing my displeasure, I'm not going to stop them, because that is their right to be an idiot if they want to. A Master Chief who was teaching Navy Rights and Responsibilities, and covering the part about the Constitution, said that while I might not agree with what you have to say, I will defend to the death your right to say it.