In short:
Flynn is being used to draw the public attention to treason so that when the documents are declassified the public will already be familiar with what criminal treason actually is.
Treason was brought up with Flynn because he acted as a foreign agent. Uneducated people hear this and cry 'Treason! Lock him up'. He did end up registering as a foreign agent retroactively, like many others in government, and therefore acted lawfully, and so has not committed treason.
This is illustrated by Judge Sullivan bringing up treason charges in one session (angrily as the news would have you believe) and then in the following session by Apologizing to Flynn for the Treason accusation (which the news left out).
The Clinton Foundation was just determined to be a foreign agent by investigators. Because it was brought to the publics attention they can no longer retroactively register as a foreign agent. They are now guilty of Treason.
Flynn was the former head of Military Intelligence. He was king of the spies. This guy just manipulated the FBI and got them to f**k themselves and their interests.