The advantage of metaphors is that they help explain things by isomorphism. The disadvantage is that people often take them too literally. Or pretend to if they want to attack the writer.
Strange as it sounds, I expected to be criticized for telling readers what they wanted to hear, not for insulting them. If you actually read the essay, the thesis is that the famous founders who are made to seem like such gods in the press are actually not that different from ordinary programmers-- that the difference, as it says in the last paragraph, is "due mostly to environment." In other words the exact opposite of the summary Atwood quotes: "Oh... you haven't founded a company? You suck."
How can so many people read an essay saying X and come away believing it said not-X? I think what happened in this case was that a lot of people who were already feeling self-conscious about working for big companies read the first section as some kind of criticism of them, and then either read that into the rest of the essay or (this is the Internet) didn't read any more before writing blog posts about it.