I think the question is not so much 'Does Al Qaeda Exist?' but rather 'What is the true nature of Al Qaeda?' There is no question that networks variously affiliated with the International Muslim Brotherhood (the Mujahedeen, Hezbollah, the KLA etc.) are engaged in international criminal enterprises (aka terrorism). The documentary did a good job of deconstructing the official myth of Al Qaeda by posing questions such as "How can it be that in Britain since 9/11, 664 people have been detained on suspicion of terrorism but only 17 have been found guilty, most of them with no connection to Islamist groups and none who were proven members of Al Qaeda?" However, it fails to conduct a more detailed interrogation of the nature of the international networks refewrred to as Al Qaeda and their relationship to Western, particularly North American intelligence networks. (It is worth noting that while the documentary does not go vry far, the very questions it is posing were (and to some extent still are) considered heresy even on the left and have always been subsidiary issues for those of us who have serious doubts about the official story of 9-11.
In part II of the story on P-tech and 9-11, Michael Kane, writing for From the Wilderness, offiers some (I think) valuable insights to the riddle (for me a better term than 'myth') of Al Qaeda. See the full article at the link below, but a key paragraphs that I would like to bring your attention are the following:-
http://www.fromthewilderness.com/free/ww3/012705_ptech_pt2_summary.shtml
"The Ptech story is of intense interest for its implications about US government guilt in 9/11. As Ralph Schoenman, Michel Chossudovsky, Paul Thompson and others have argued, "al Qaeda" is not only traceable to CIA activity in Pakistan and Afghanistan during the Soviet period, it is also a current tool of American imperial ambitions. That directly contradicts the official story, in which al Qaeda is the foreign devil incarnate, a militant hate group formed straight from the soil of Saudi ideology - with no economic grievances, no interests in common with anyone in the non-Muslim world, and above all, no connections to the United States through funding, personnel, armaments, drug trafficking, visa assistance, or communications. It certainly is a militant hate group, but the rank and file may be totally unaware of real connections between their own leaders and the people they oppose with their very lives. These disturbing links would be just as agonizing - and just as unthinkable - for American citizens as they would be for a militant Islamist teenager in a ski mask jumping hurdles at some secret training camp.
"Beneficiaries of the Ptech-connected MAK charities, the young men in Hezbollah and Hamas are fighting in land disputes, not heady ideological quests. They are also bitter, bereaved, murderous bigots with all the psychic rigidity and hysteria found in fundamentalists from Oklahoma to Hebron to Jeddah. Their hatred of the American national security state is surely absolute, but they are also beneficiaries of the Pentagon's need for an Enemy. That means that they can expect the United States to provide covert help of some kind at crucial points in the game. And the most despicable element in the American side of that process is the Bush-Cheney junta itself, which used its own assets inside the terrorist network associated with Osama bin Laden to murder three thousand civilians in New York, Washington, and Pennsylvania as a pretext for unending warfare. This was done for reasons of state. But it was also done for personal gratifications including vast sums of money, permanent blackmail over those involved, and a heroin-like rush of criminally insane individual power. Sophisticated or naïve, cynical or grandiose and idealistic, each person involved betrayed humanity. And the apparatus that permitted this remains in place - as do most of the personnel."