Two positive things to say about that video:
1) QualiaSoup obviously has a very analytical mind and - unlike most people I come in contact with - he has founded his logic upon very concrete definitions, and establishes those definitions within the video. When I take issue with someone on this forum or elsewhere, it is usually over their inadequate definition of the words they are using.
2) Fantastically helpful and easy-to-follow visual aids. Many of us could follow his words via radio broadcast easily enough... the presence of such great illustrations and diagrams makes this video understandable by a great many more people, especially people who are not avid readers.
I think the misunderstanding of atheism stems from the presence of people who are in fact opposed to the existence of any god - "belief that no gods exist" - and the fact that such people are often the most vocal, while the "silent analytical majority" on both sides of the metaphorical theistic fence usually weighs in with a more muted tone. The majority is then lumped in with the more extreme among their respective theistic/atheistic proponents.
That's usually how things work in other arenas, too, especially political ones.