I'm particularly curious as to what kept the soldiers of the HRE from joining with the peasants- it seems to me that most of them were peasants themselves, so why wouldn't they be sympathetic to the cause?
Have you read what the causes of the Peasants Revolt were? The situation in the HRE was not nearly as simple as classifying people as peasants or knights or nobles. Even if it was possible to do so, the decision to join a rebellion is never as straightforward and deterministic just due to one's social class.
The Peasants Revolt had very strong Anabaptist strain and a manifesto that included the right to form their own church hierarchy, tithe for public use, and abolition of serdom, regulations against use of land and forests. Not all of these are agreeable to all peasants.