While Web 2.0 is indeed a media-coined term, sites can still be categorised under this banner.
The article holds truth one way or another - the problem is that people are consciously AIMING for a "Web 2.0" design (you know the type) with lots of flashy stuff such as Lightbox, AJAX; basically JS that doesn't degrade and non-standard design elements in an attempt to be different, but in the end just confusing the user. Because people are aiming to earn the "Web 2.0" title as it's in vogue, there is an inherent ignorance of good web design practice, even though the central aspect of "Web 2.0" is user experience - and most "Web 2.0" services use this as a selling point.
The article definitely has a point, and even though "Web 2.0" was originally hyped by the media, designers have used this as a selling point and jumped on the bandwagon, effectively solidifying its existence.