I'm not sure which particular battle you're referring to but it is true that the professional, smaller armies of The Truchesess fared much better than did their opposition in battle.

One of the answers is organization. The enemies of the peasant bands, Georg, The Truchesess who led the reaction against the peasants had professional soldiers and relatively many artillery pieces in comparison with the peasants.

It was very, very difficult for armed peasant bands to achieve anything near their discipline and professional capability. This is mostly due to the reality of the 'Gemeinde' the peasant village community. The peasants needed able hands in their local communities to take care of farming and other peasant stuff which i have no practical understanding of.

For example the peasant band of Alsace organized themselves according to a rotational principle. A group of peasants would be 'in the field' for days or weeks before being switched out so they could get back to their communities (Hoyer, 1979, p 107-8).

As you can imagine this impeded unit cohesion and the ability to build discipline and experience.

There are also political reasons for the defeat of the peasantry though. The aspiring bourgeoisie of german cities did quite the political balancing act in trying to avoid direct opposition to princely authority while also avoiding peasant aggression. As such their allegiance was very shifty.

For example the Peasants of the Werra Valley were betrayed by the city council of Eisenach. The council pretended to mediate between the peasants and Phillip of Hessen but instead chose to arrest all the peasant negotiators who turned up (scott 1991,p 42). The extemely wealthy, mine-owning family Fugger also lent the Schwabian League 10.000 florins at a critical moment when it was difficult to raise the neccesary troops to combat the intensifying rebellion.

Sources: Hoyer, Siegfried. "Arms and Military Organisation in the German Peasant War" in The German Peasant War of 1525: New Viewpoints, 98-108. London, 1979

Scott, Tom. The German Peasants’ War. New York: Humanity Books, 1991