Maybe this is getting into a No True Scotsman argument, but that permit was not for what's often considered to be antifa. Being a counter-protester is not automatically antifa. From the link you posted:

> Walt Heinecke, a professor at the University of Virginia, told Moyer that he received a “special events certificate of approval” for events at McGuffey Park and Justice Park — sites blocks from Emancipation Park, where white nationalists had a permit for a Saturday rally.

Antifa, the group that is more commonly associated with things like Richard Spencer in the face, seems to be more informal: https://www.vox.com/identities/2017/1/26/14369388/richard-sp...

Edit: Another example of what's associated with antifa: punching journalists http://www.dailymail.co.uk/news/article-4785564/Reporter-pun...