Because (((they))) know there are unstable people in this world who may take Flynn's general statement as some sort of "Go Order". If that happens, "Q" can catch the blame as a domestic terrorist group, giving the DS justification for targeting "Q" adherents, while Flynn (controlled opposition) let's them swing in the breeze. The DoD has already stated they will not pursue any further actions against Flynn, effectively giving him immunity to bait ordinary citizens into violent action.
Be careful who you follow.