The Significance of the Excerpt Below
(1) It demonstrates that the Scottish practice during the days of the Westminster Assembly was for the congregation to say an audible ‘Amen’ after prayers, per Scripture’s prescription.
(2) It answers the perennial question of humble saints whether we can say ‘Amen’ to prayers where there is a mixed crowd of ungodly people, who are also saying ‘Amen’. Mr. Coachman, below, was a Separatist; Rutherford argues against him.
Due Right of Presbyteries 1644, chapter 4, Section 5, Question 3, pp. 236-7
Mr. Coachman: “How can any godly man consent or say ‘Amen’ to such a holy action [public prayer in a worship service], when it is jointly done by such as, for the most part, are the enemies of God?”
 Mr. Coachman, Cry of the Stone, Sect. 4, p. 11
1. This makes [argues] against the man [Coachman] and the churches of New England, for they admit constantly to the hearing of the Word, and so to the prayers of the Church, those who are not received members of the visible church. How can any godly man say ‘Amen’ to the action of hearing the Word, when it is jointly done by God’s enemies?
I prove the antecedent: The unity of faith, hearing one word of Faith [the doctrines of Christianity] preached (Eph. 4:5), makes a visible body in profession, even as the joint partaking of one bread and one cup in the Lord’s Supper makes one body, by obsignation or sealing (1 Cor. 10:16-17).
2. Division of hearts in hearing (while some follow Paul, some Apollo, some Cephas) makes a schism and division in Christ’s body (1 Cor. 13). Therefore, in hearing one and the same Word preached, there is a visible Church-union. For all division of that kind presupposes a union and unity in a visible incorporation.
3. 1 Cor.14:26, ‘When ye come together’ (as one Church body) ‘every one of you has a psalm, has a doctrine.’ Verse 4, ‘He that prophecies edifies the Church.’ Verse 31, ‘So you may all prophecy one by one, that all may learn, and all may be comforted.’ Verse 35, ‘It is shame for a woman to speak in the Church.’
Therefore, the saints that meet together in one Church to be edified and comforted by doctrine and hearing of the Word, do all jointly perform an action of hearing and learning of the Word of God, and are in that one Church and one visible body, and are called one Church (verses 4-5), that the Church may receive edifying:
Verse 12: ‘Seek that you may excel’ (by prophesying) ‘to the edifying of the Church.’ Verse 23, ‘If therefore the whole Church come together, unto some place, etc.’ Verse 28, ‘If there be not an interpreter, let him keep silence in the Church.’ Verses 34-35. And these who understand are all to say ‘Amen’ to that which is prophesied (verses 16-17).
And yet that action of hearing and saying ‘Amen’ to the Word preached and to the prayers of the Church, is done by many unregenerated who are yet in the state of enmity with God, as our Brethren grant in that they do admit all to be a church and one church hearing the Word preached.
“But how can they say ‘Amen,’” (says he) “to a holy action done by God’s enemies?”
I answer: This objection is no less against Paul and the Word of God than against us. For many enemies to God, whose hearts are rocky, thorny and stony ground, do hear the Word of God, and that by God’s commandment (Matt 13:2-5, etc.). The deaf and the blind are commanded to hear (Isa. 42:18; Isa. 28:9,10). And these, whom God has covered with a spirit of slumber, are to hear the words of the sealed book (Isa. 29:9-11), even those who stumble at the Word and fall, and are broken (Isa. 8:14-16; 1 Pet. 2:8).
“What godly man can say ‘Amen’ to such a holy action as is performed by God’s enemies?”
2. The godly say ‘Amen’ to actions of God’s worship in two ways [either rightly or wrongly]:
1. [Rightly:] As it is the ordinance of God enjoined and commanded to the wicked and hypocrites no less than to the godly. And we are to countenance their communicating [in prayer] as we do their hearing of the Word, and to join with them both in our real and personal presence and say ‘Amen’ with them, [just] as the disciples gave their personal ‘Amen’ and their countenance and presence to a holy action at the Last Supper with one of their number whom they knew to have a devil and to be a traitor. And [they] dipped their hand in the dish with this man after Christ had warned them that there was such a one. But this is but to say ‘Amen’ to the external worship, which is lawful, according to the substance of the act.
2. The godly may be thought to say ‘Amen’ to the actions of worship performed by the enemies of God,by approving, allowing, and commending the manner of their performing the holy actions of God’s worship. That is, they may be thought to approve the manner of their hearing and receiving the sacraments, that is, when they approve their performing of those holy actions without faith and with wicked hearts and hands, and when they allow that they eat their own damnation.
Thus [in this second way,] no godly man can say ‘Amen’ to holy actions performed by God’s enemies. Nor is our external communicating with them, a saying ‘Amen’ to the wicked manner of receiving the seals. This is most unreasonable, and cannot be proved by God’s Word.
On Saying ‘Amen’ After Prayers