The point of the ".01% of comments" argument is not to justify those comments, but to illustrate that sexism does not seem to be integral to FOSS. The same argument can be made using your 10% black argument; if 10% of FOSS developers are black, and only 1% of comments or discussions have racist overtones, it can be safely assumed that racism is not an integral part of the FOSS movement.
Of course there are sexists involved in FOSS, just as surely as there are racists, homophobes and any other type of bigot one can imagine. FOSS is made up of the whole, world-wide body of people who choose to participate; there is absolutely nothing standing in the way of a neo-Nazi who wants to upload the mp3 player s/he just wrote.
The author of the article, on the other hand, is making FOSS sound like an organization whose leaders are specifically not allowing women to participate. When the only thing necessary to participate is a computer, an internet connection and the will to program something that will be distributed for Free*, the concept that anyone at all can be kept out against their own will is patently ridiculous.
Maybe women aren't by-and-large attracted to FOSS. Maybe there are social pressures that discourage it. Maybe women who ARE interested find it more difficult to join a particular project because the people who run that project are, themselves, sexist. None of these things are even remotely reminiscent of the intrinsic sexism that was present in, say, 19th and 20th century business. It's a hell of a lot easier to start your own project fork on github or freshmeat than to break into an industry where your clients are as likely to be sexists as your competition.
Anyway, even if there are sexists involved in FOSS (pretty much guaranteed, as is any other form of bigotry), the fact that they exist does NOT indicate an "industry prejudice".