Hi, I'm one of the authors. I can certainly see why you'd take it as condescending. At the time, it was generally taken in the sense that we meant it: we were trying to articulate what Web users understood but the media and most businesses weren't getting.

Remember that in 1999, the Web wasn't as mainstream, and many users felt that being on the Web was a special experience. There was an "us vs. them" feeling, where the "us" were people enthusiastic about the Web and excited about how it was (we thought) transforming our lives, our culture, and our institutions. So the clues were absolutely not for our readers who, we assumed, were part of the Web "us," but for the media and businesses who weren't on the Web or weren't part of the Web culture, and who yet were attempting to impose their understanding upon it.

Now the Web has become such an accepted part of everyone's lives in our culture that it doesn't feel nearly as much like Us vs. Them. I think that explains why the Manifesto now reads as condescending, whereas at the time it was taken (at least by the readers who liked it) as an articulation of what they already felt.