The religious wars of the 16th and 17th century delegitimised the princes as well - in the eyes of those who chose the other faith. The whole 30 years war was about princes waging war against each other in denial of the other's attempt to set the faith for his realm.

China also has a huge history of rebellions that did not necessarily rest on organisations.

Decolonialisation rebellions were also often rather based on the idea of sovereignty than on organisations.


It was never easily tolerated when rulers killed off troves of dissenters. That's now a new thing. Today we bother more about it because of the media (nobody cared about Japanese imprisoning Koreans in 1920, but now we care about the gulags of the North Korean regime).
The people in the country themselves don't need mass media to learn about what happens with their neighbours, of course.


In the end, rebellions succeed when a regime is ripe for failure. I'm not even sure organisations are helpful against such regimes because organisations are usually badly infiltrated and can be destroyed much more easily than ideas.