Ver. 6. Charge, or declare; or by the Greek, we command. — In the name of our Lord. This may signify a separation by excommunication. (Witham) — That you withdraw, &c. St. Chrysostom upon this place, St. Augustine, Theophylactus, and others understand St. Paul as speaking of a kind of excommunication. But St. Chrysostom on ver. 13. and 14. seems to restrain its meaning to a prohibition for the guilty to speak to any body, unless they spoke to him, if their conversation tended to exhort him to repentance. Theophylactus likewise remarks that this punishment was formerly much dreaded, though now not in use.
It could be applied that way, but you also have to consider that most Protestants have NEVER RECEIVED apostolic teaching. They persist in faithful pursuit of the amount of revelation they have received. It is not that they had the teachings, then left, but they never were aware that there were any apostolic teachings. Most of them believe the bible is the only source of divine revelation.
If I were to guess I would say that means dont hang around PUBLICLY with such people who are living an immoral life as it will give other people the wrong impression of how Christians live. Also, dont hang around them if you yourself are weak because you could easily get pulled down to their level.