I generally disagree with the tone of this article. It suggests that there actually is a problem. The landscape of the web is flat due to history and its general usage and purpose. It serves “everything.” The App Store on the other-hand (mostly) serves Mobile. The graph that shows Facebook at the top and Skype at 10th is because those are social / time-consuming apps.
However, take Uber for example which is likely not even in the top 1,000, is still doing quite well as a business (probably better than Skype). All of their transactions happen on a Mobile Native App, not a website.