Unless you are doing cutting-edge research in your daily job, you are not much different from those indies working on "superficial crap", apart from the fact that being "part of a company" gives you the illusion that it's more legitimate. Was google search or skype superficial and trivial? They started as programmer toys. The point of the article is that a programmer can start with $0 and build the whole product. A programmer is like a farmer or an artist, a de facto entrepreneur.
Both Google and Skype were more then "programmers toys" they started out as solution to actual problems: how to find useful things on the web, and how to connect to other people through the internet.
Also, nothing is stopping you from using your software chops on cutting edge research projects. The issue is that the required skill sets are usually different then the latest Web 2.0 technologies.
