The single word “amen” is an affirmation of what God positively wills or of his permitting something to occur (for a still greater good). It reminds us of St. Francis de Sales remarking that if we knew all that God knows, we would will to happen exactly what does happen (see also Rom 8:28).
—from Prayer Primer: Igniting a Fire Within by Fr. Thomas Dubay, S.M., Ch. 5: Elegant Variety