(Note, I am from the United States, so my comments will reflect that particular perspective)
The fact that the United States' flag is such an important symbol, and that so many are deeply offended by public displays of disrespect toward it, is all the more reason why it is vitally important that flag desicration remain protected. The framers of the Bill of Rights did not enact the First Amendment to protect the right of people to express popular viewpoints -- they enacted it to protect unpopular viewpoints. They enacted it to protect the rights of each particular person to express ideas that might offend people.
It is hard to believe that I'm not preaching to the chior here (perhaps I am). We are all fans of this particular website, or we wouldn't be here. Consider, however, the fact that many people find the content of this site immoral and deeply offensive. Suppose the government were to attempt to outlaw accessing this site for that reason (the offensive nature of BDSM). Everyone here would, I'd bet, be complaining that their "free speech" is being trampled upon.
The First Amendment is a two-edged sword. Not only does it ALLOW you to utter and listen to speech that might offend your next door neighbor, it also COMMANDS you to tollerate your next door neighbor's offensive speech. As many very patriotic people have pointed out, "freedom ain't free." Usually when people say that, they are talking about military service, but it means something even more fundimental than that. It means that if are really serious about Freedom of Speech, it is every America's patriotic duty to follow the command of the First Amendment and tollerate the most offensive speech you can possibly imagine.
Sorry for the rant -- the above is a pet peeve of mine.