The Gemara in Sukkot 43b presents the following story (rough translation):
One time the 7th day of Sukkot fell out on the Shabbat and bundles of Aravot were brought out before the Shabbat and placed in the Temple courtyard. The Baytusim (A sect that disagreed with the Rabbis regarding the ruling that the custom of the aravot is done even on Shabbat) noticed this and placed the aravot under rocks (The rocks are muktze and can not be moved on the Shabbat so the aravot could not be used the next day). The next day Amei HaAretz (ignoramuses who were presumably not knowledgeable in the laws of muktze) noticed the aravot and removed them from under the rocks. The Kohanim took the aravot and placed them at the sides of the Temple alter.
In Moadei Reiya, pg 111-113, Maran Harav Kook Zt"l explains this story as an example of how the natural instinct of the common folk, ignorant in Torah but for whom the honor of the Torah is of great importance, saved the Rabbis from a tremendous dilemma. If the Rabbis would have instructed to remove the aravot from under the rocks, this would have been seen as an abolishment of the laws of muktze. If on the other hand the aravot would have not been used, it would have seemed as an agreement to the position of the Baitusim.
The natural instinct of the ignoramuses was to simply undo the insult that the Baitusim inflicted upon the sages. These simple Jews, not knowledgeable enough to understand all of the Halachic issues involved, can be a positive force in the world. A natural Jewish instinct is an important (though not sufficient) quality in a healthy spiritual life.
When we beat the arava on the ground, we are not punishing it. Rather we are demonstrating that this natural instinct (represented by the arava that in turn represents the ignoramus who respects the Torah) is a real force in the world and can be the cause of good. This force must be respected and channeled towards constructive ends.
