Do you say ‘Amen’ after prayers?  It is a way we show our audible consent to what is prayed, and join therein.  The significance of this Rutherford quote is two-fold:

(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.   

Rutherford on Saying ‘Amen’, No Reason for Separation