The wheat on Jesus’ threshing floor is the righteous, while the chaff is unrighteous. Christ will separate the two groups (Matthew 25:31–46). The chaff are not the sins of the righteous, but the wicked who grow up, in this world, with the wheat, to eventually be separated by judgment (see Matthew 13:24–30; John 3:18–21). Matthew 3:11 teaches us that this separation already begins with the church now.
The wheat signifies the righteous and the chaff signifies the unrighteous. In his judgment Christ will separate the righteous from the unrighteous, according to Matthew 25:31–46. After all, it is not the case (as some seem to suggest) that the chaff references the sins of the righteous, but rather the case that the chaff and the wheat are at first joined together only to be separated by judgment (see also Matthew 13:24–30 and John 3:18–21). It is important not to read too much into this, however, but rather keep the focus on John’s preaching of deliverance through judgment. Matthew 3:11 teaches us that the church in her full earthly manifestation is saved thereby.1
12 His winnowing fork is in his hand, and he will clear his threshing floor and gather his wheat into the barn, but the chaff he will burn with unquenchable fire.”