True, there are groups that have claimed to be anti-fascist and have protested the administration's actions. But much of this activity has been spontaneous rather than organized. The word "Antifa" is more of a derogatory term from the right than a term used by an organized group with countable members.
Because of the fuzziness of what Antifa actually is and who counts as a member, this EO gives the federal government the ability to label people as domestic terrorists using a very broad definition. Given this administration's habit of pushing the bounds of its interpretive authority, I worry that this will have a chilling effect on protected political speech and protest.