Protest in the public square is the ultimate American act; there's a quote from a movie from the Nineties (Rude Awakening) where a protester's patriotism is challenged and he replies: I am a patriot; I love my country; I am duty-bound to make it better.
On either side of the issue are either the blind "patriots" who see nothing America does as ever being bad and those who, for some reason, really despise America and see nothing good in it. Both attitudes are, ultimately, unAmerican -- and pretty stupid.
The anti-war protesters who have an honest belief that their country is doing something wrong in Iraq have not only a right but a responsibility to speak out against it. I think they're misguided and naive, but that doesn't make them less patriotic.
On the other hand, there're those who are simply opposed to anything American; those who've never been proud of their country in their adult lives and still aren't (because their spouses aren't running for President yet, I presume). They aren't patriots for speaking out, they're enemies.
This protest was likely made up of both groups, but only the latter made it into the final video, because that's what the filmmaker wanted to portray. There's nothing inherently wrong with that, it's the nature of documentary film-making that the clips that support the creator's agenda are those that are included, but it is why all documentaries, especially those you agree with, should be taken with a grain of salt. The exception to this rule, of course, is anything by Micheal Moore, which should be taken with Pepto Bismol.