Don’t confuse web apps (programs that happen to run inside your browser) with web sites.
The best way to use gmail or pages/keynote (or Office if MS ever makes it available) on a mobile device is with a mobile app, no doubt. Ditto for any other web app.
The apps that Jeff complains about in his post, however, are “you’re visiting our website from a mobile device, why don’t you download our app instead!” apps, which are a complete waste of the user’s time.
Suppose someone sends me a link, or I’m looking for something and I google and click on a search result. The resulting web site “helpfully” offers to take me away from the thing I wanted to look at to the App store. Which, if I download it, the resulting app will not be smart enough to take me to the link I was originally trying to get to. To hell with that.
Or suppose I want to use Ebay (just as an example of a highly interactive web site where I’m not just going to end up there because I clicked on a link). I downloaded that app back when I first got an Ipad, only to discover that it didn’t include support for seller features or advanced search features that I use just about every time I interact with Ebay. For all I know the ebay app may have gotten better since then, but having wasted my time once, I am disinclined to waste it a second time.
My phone is a dumb flip phone, so I cannot speak to how useful apps are compared to websites on a tiny screen. But on an Ipad, the web browser is far more useful than an app version of the website nearly 100% of the time.
The deplorable state of most web sites when it comes to being optimized for viewing on a mobile device is a whole nother topic, of course, but the solution to that problem is implementing proper adaptive site design, not trying to steer your visitors to a crappy app version of your site.