The American Revolutionaries were Traitors to the Crown.
The Council of Truth affiliates with the Sentinels and Red Freedom, which have employed terrorist tactics. Therefore, anyone affiliated with the Council of Truth (which is not a recognized governing body on Rubi-Ka) is a terrorist.
This is why the Neutrals can operate outside of the Omni-Tek Machine without being branded enemies.*
*ignore the ridiculous Tarkhan Doctrine.