There are seven layers according to the OSI model. The TCP/IP model simplifies this into "above layer 4", layer 4, layer 3, and "below layer 3". In practice, TLS/SSL is an implementation of the session layer (layer 5) with other protocols run on top in the application layer. The data link and physical layers don't map particularly well to LLC, MAC, and physical transmission technologies but they serve as a reasonable approximation. The presentation layer (layer 6) doesn't really exist but neither did the session layer until a need for encryption inside of TCP came along. Onion routing could be argued to be another session layer technology. The real world is messy and simplifying it into four (or five) layers of nested protocols puts TCP/IP on a pedestal. So take the title with a grain of salt.

The original article argues that cryptocurrencies are a layer of protocol, wrapping those above it. Looking at NameCoin, it isn't an argument that should be dismissed out of hand.