Nice points RR, but the Founding Fathers did not write the first ammendment to protect hate speech, to protect the rights of the KKK, to allow Martin Luther King to address prejudice, or to allow someone to scream fire in a theater. They wrote it to protect specific events, which were the ability of the American people to protest against their government. I would like to think that the Founding Fathers were smart enough to know that government can't control feelings of hatred or dislike between people, but more likely they didn't even consider the issue. They were out to prevent the United States from becoming like England, where people who opposed the government, in speech or in press, were persecuted.
Over the years, various legal precedents have altered the 1st ammendment and expanded its purpose, much like those a-holes in the Supreme Court unjustly expanded the 5th ammendment.

So everything that "conventional wisdom" says is now covered by the 1st ammendment is a: not necessarily what the Founding Fathers wanted protected, and b: subject to reconsideration at any time. If we were to follow your example, that the ACTION of burning an American flag (a violation of US law) in order to protest the US Government is legal, then we would have to accept that the assassination of an American politician (also a violation of US law) in order to protest the US Government would also be an action protected as "freedom of speech." Under your understanding the ACTION of murdering three civil rights advocates as a means of protesting the end of segregation laws would be protected as "freedom of speech." You see what happens when you expand the scope and meaning of a well-worded and concise principal?
Since the US Code clearly spells out that it is a crime to desecrate or destroy the flag, then what a flag burner is doing is violation of Federal law. The 1st Ammendment says that you can speak your mind, you can write and publish whatever you want, and you can seek redress if you suffer damages... it does not cover taking ACTIONS such as burning flags, assassinating leaders, or breaking any laws. And just as the American judicial system can expand through precedent the meaning of an ammendment, the legislative branch can tighten it back down, and in this case they're right to do so.