In reality, peasants in Edo period Japan probably had it better than peasants in other feudal cultures. During the Edo period, the Samurai lived in the cities separated from the common folk, and so the peasants really had no contact with their absentee overlords, and therefore didn't feel so much like oppressed subjects of the Tokugawa regime. Generally speaking, as long as they obeyed the rules and paid their taxes on time and in the amounts specified, they were left completely alone. Villages were self-run, with headmen appointed (or depending on the area, hereditary) and networked with surrounding villages; they were very well connected and organized at the local level. Local villages relied on each other for support during lean years, or as local markets for goods and services. This level of local organization actually lent itself quite well to mass protest. For villages that were tightly organized, a protest or petition was a simple thing to throw together.
Organized protests were "illegal", but there were prescribed measures for registering protest - the ability to petition one's lord. The Tokugawa government was generally fair, and subscribed to Confucian values, and so tended to treat the peasantry as their "children". And so the peasants, for their part, paid the taxes and obeyed the laws in return for the benevolence granted to them by the lord. Although petitioning was an acceptable form of protest, improperly worded petitions were illegal and grounds for execution. The required form of petition usually went along the lines of asking for assistance from the benevolent lord in order that the petitioner may "continue to live as a farmer". Demands and complaints were patently illegal.
The first line of petitions/protests fell on the local representative, who decided right then and there if the petition was valid and if it would be passed on to the local lord. If it didn't make the cut, peasants were for all intents and purposes SOL when it came to legal recourse. We'll get to the illegal kind in a second, but if the petition was accepted, it would be looked over by the lord, or more likely first line of bureaucrats, and granted or not. Often it involved pleas to lower taxes during times of famine or crop failure, or requests to not be liable for transporting taxes all the way to Edo, or requests to pay taxes "in kind", i.e. if you're a silk producer, being allowed to pay taxes in silk, rather than have to convert it to rice first. Things of that nature. For the most part it seems that requests for temporary reduction of taxes would be granted - because, if you tax your tax base to the extent that they can't feed their families, you were asking for trouble - at best they might flee your domain, leaving untended farm plots that couldn't be farmed, and therefore taxed. At worst you might find yourself with petitioners going over your head to the Bakufu (which reflected more poorly on the local lord than the peasants) or armed uprising.
On the one hand, going over the lord's head was a suicide mission, as the Japanese were sticklers for convention - and often the leaders were executed - but on the other hand, this was often effective in the long run. On more than one occasion, Samurai lords were dispossessed of their lands due to chronic maltreatment of their peasantry and replaced with more lenient benefactors. In fact, protests were surprisingly successful, as peasants rarely protested without good reason. If they were able to eat and able to support their families despite the taxes they were paying, things were good. They were essentially self-governed, and so unless things really became dire for them, there really was no impetus for mass protest.
When things really hit the fan, and things got so bad and peasants got so fed up, but domain leadership was being unresponsive, protests were inevitable. They were more often than not led by upper class respected commoners, and consisted of all the area villages. Village headsmen declined to participate at their own risk, as they themselves might find their own property and livelihood the target of peasant rage. Things rarely got violent, however there are many examples of peasants destroying the homes of merchants, moneylenders, and landlords in what in basic terms was a targeted redistribution of wealth. They were often engineered to take back lands taken by debt, or to return pawned goods to the rightful owners. Often these changes would stick. In most cases, when push came to shove, the local lords would side with the peasants for utilitarian reasons. Lords didn't necessarily get a cut of profit from money lenders or pawn brokers, and so had no financial incentive to side with them, but had all the reason to side with the people that paid them taxes.
When the local lords were the problem, things got more complicated.
Plenty of information about the rebelliousness of the Edo period can be found in Stephen Vlastos' book Peasant Protests and Uprisings in Tokugawa Japan as well as the discussion thread for this book on the Samurai Archives Japanese History Forum.
