What surprises me the most is that this came from the author of the paper, not the publisher. In my experience, authors don't see any kind of royalties from any

What surprises me the most is that this came from the author of the paper, not the publisher. In my experience, authors don't see any kind of royalties from any publication fees, and generally there are even fees (often significant ones) associated with having your work published in a journal. Generally, if you're the author of a given paper, you'd prefer if your paper were published for everyone to read (even beyond the intangibles, this could increase citation count), whereas the publisher is the one with an incentive to keep it gated. In fact, some journals are now offering creative commons licensing as an upsell - pay a certain amount of money and there's no paywall on this article. This EFF article may be playing a bit fast-and-loose with the term "article", though. I'm seeing something here about how it was actually someone's thesis, and that the author was concerned that the person who put it on Scribd did so in an attempt to profit off of some sort of system of fees. It's not clear to me why it would go as far as prosecution, though, unless issuing a takedown request necessitates full criminal prosecution...