Care to elaborate? I feel that I went out of my way to provide a number of pertinent examples.
I pointed to the trend of traditional web properties moving to native apps when it came to mobile. Things like nytimes, economist, and even Facebook.
I discussed how most new social networks on mobile that have gained any traction or attention (such as FourSquare and Path) were largely a native phenomenon (even Google+ chose to have a native iPhone app).
I talked about very real examples of how Flash was important in the development of the web.
I believe that there are a lot of valid counterpoints to my argument, and I'm actually really interested in hearing and thinking about them. However, I don't think hand-waiving it away as "theology" is one of them.
I thought this was very well written and clear. These authors bring up a very valid point. Not really sure if the web can reinvent itself. Java applets and Flash both failed along the same lines. Maybe the web (and HTTP) is only good for relaying information and rich experiences will always be native. It doesn't have to be that way, it just is.