The general tone of the NPRM seems to be that an ISP can and will block or throttle any non-web or non-email traffic. That could include any peer-to-peer innovations that seek to restore the original functionality of the internet, such as those mentioned by the author.
On the contrary, the dissent by Commissioner Clyburn specifically mentions Skype as an example of internet usage. He believes the traditional notion of "permission-less innovation" is under threat from the Chairman's proposed approach.
https://apps.fcc.gov/edocs_public/attachmatch/FCC-17-60A1.pd...
The author highlights the importance of distinguishing "the web" from the internet. Perhaps nothing is more important. The internet has more value than the web. The web is severely limited in functionality. The internet, still underexploited in its potential, does not suffer from the same limitations.