What is "Charutz"?
Rashi: It is a tree called Morag. It has many grooves. It is used to cut chaff to become straw.
Radak: It is a wooden board with small stones inserted underneath to thresh.
Why does it say that Ketzach is not threshed with Charutz?
Rashi: Ketzach's seed comes out of the straw easily. There is no need to thresh it with Charutz. Similarly, one need not 1 turn a wagon wheel to thresh cumin. It suffices to bang them with a staff.
Radak (29): After seeding, one must wait a set time for them to sprout and ripen, and hen he threshes and takes out the food. So Yisrael learned Chachmah, Torah and Mitzvos, and got used to them. They should have grown wise and fixed their deeds, so nations would say "Rak Am Chacham v'Navon ha'Goy ha'Gadol ha'Zeh" (Devarim 4:6). Threshing is the Navi's word and warning, to take out the fruit. A little should have sufficed, like for Ketzach and cumin. However, the nation needed great warning, like grain needs great threshing.
Malbim: Now it begins to explain individual's afflictions. Even after seed grew successfully, one must thresh and grind it to remove the chaff and clean the grain. Also a Nefesh prepared to receive creed and Musar, sometimes they are mixed with errant teachings and false ideas from intellect and imagination. One must remove the chaff, and clarify the Emes from the Sheker. Some chaff does not cling so much, and is separated through threshing and beating. Some is firmly attached, and one must grind and sift to separate it. Similarly, errors and foreign mindsets due to imagination are easily removed. Intellectual mistakes via misleading philosophical teachings and errant assumptions are harder to remove 2 . One needs "v'Tzadik be'Emunaso Yichyeh" (Chabakuk 2:4).
Radak: "Lo" applies also to "Ofen Agalah