It makes sense that the army crushes them, but the majority of soldiers in medieval European armies were levies. How then were they put down? Were mercenaries used?
Most of the army weren't necessarily levies, and even if they were, they were probably freemen or people from towns, rather than serfs.
Mercenaries were indeed used, probably more than levies, especially later on in the middle ages.
During the Jaquerie rebellion in France, the nobles rallied together and basically ran down the peasant army with heavy cavalry, though not before the peasants burned some local manors and killed the landowners and their families.
After the battle, knights and mercenaries roamed the countryside, hanging random peasants, burning things, etc.
In terms of revolts, towns and cities with walls were more likely to resist the (often rural) nobility compared to peasants in the countryside.