Ye root up also the wheat - They so much resembled the true wheat that even then it would be difficult to separate them.
By gathering them, they would tread down the wheat, loosen and disturb the earth, and greatly injure the crop. In the harvest it could be done without injury.

But he said, Nay - God judges quite otherwise than men of this mixture of good and evil in the world; he knows the good which he intends to produce from it, and how far his patience towards the wicked should extend, in order to their conversion, or the farther sanctification of the righteous. Men often persecute a true Christian, while they intend only to prosecute an impious person. "A zeal for the extirpation of heretics and wicked men," said a pious Papist, "not regulated by these words of our blessed Savior, allows no time for the one to grow strong in goodness, or to the other to forsake their evil courses. They are of a spirit very opposite to his, who care not if they root up the wheat, provided they can but gather up the tares." The zeal which leads persons to persecute others for religious opinions is not less a seed of the devil than a bad opinion itself is.

But he said, nay,.... The answer is in the negative; and which, if spoken to angels, is to be understood, that they should not inflict punishments, or pour out, their vials, as yet, on formal professors, lest the righteous should share in them; and if to magistrates, the sense of it is, that they should not persecute with the sword, or put men to death for heretical opinions; but if to ministers of the word, which sense I choose, the meaning is, that not everyone suspected to be a tare, or a nominal professor, is to be removed from the communion of the church, because there is often danger in so doing:
lest while ye gather up the tares, ye root up also the wheat with them: not that men of openly scandalous lives are to be tolerated in churches; they are to be withdrawn from, and put away; nor men of known, avowed, heretical principles; such, after the first and second admonition, are to be rejected: yet there may be such in churches, not altogether agreeable in principle and practice, whose character and situation may be such, that there is no removing them without offending some truly gracious, useful persons, in whose affections they stand, who may be tempted, by such a step, to leave their communion; and so cannot be done without a considerable prejudice to the church. The scope of the parable, and the design of our Lord in it, are chiefly to be attended to; which are to show, that a pure and perfect church cannot be expected in the present state of things; and that saints should not be immoderately uneasy, but patiently bear such exercises, until Christ's time is come to relieve them, when the tares and chaff shall be separated from the wheat; when sinners shall not stand in the congregation of the righteous, and there shall be no more a pricking briar, nor a grieving thorn in the house of Israel.

But he said, Nay--"It will be done in due time, but not now, nor is it your business."
lest, while ye gather up the tares, ye root up also the wheat with them--Nothing could more clearly or forcibly teach the difficulty of distinguishing the two classes, and the high probability that in the attempt to do so these will be confounded.

Nay; lest . . . ye root up the wheat also with them. The roots of the wheat and tares were often so intertwined that one could not be pulled up without the other.