When God warned Joseph in a dream to flee to Egypt, sometimes asked why God didn’t warn the other families? Some consider it cruel for God to allow this.
This goes to the heart of a very great mystery, the problem of evil. It is an unquestionable fact that God permits a great deal of evil to go on in our world and very seldom does He intervene to stop it.
We know that God permits evil as a “necessary” condition of freedom for the rational creatures He has created. Angels and humans have free and rational souls and, if our freedom is to mean anything, it must be that God allows some angels and men to abuse their freedom, and even become a source of evil and temptation for others. Were God to routinely step in every time one person does something God does not want, it could not be said that we are really free. And if we are not really free, we cannot love. And if we cannot love, we are not lovers, nor sons and daughters, but slaves.
As such, this life amounts for us as a kind of test wherein God permits some degree of evil to flourish, yet not without offering us the grace to overcome. It is also clear that, on account of temptations and trials, our “yes” to God has greater dignity and merit than if we lived in an essentially sin-free zone or paradise.
Further, it is a general rule of faith that while God permits evil, He can draw a greater good from it.
Many of us, who have remained faithful to God, are able to look back and see how our sufferings also brought strength to us, and even known goods. Surely, too, there are many unknown goods that God is able to draw from the difficulties and evils of this world.
As for the death of the Holy Innocents and God’s “failure” to warn other families, we can only apply such norms. We are not in a position to really say what was best for God to do. It is clear that God allowed the torture and death of His Only-Begotten Son to bring great good. It is also clear that God has chosen to associate many martyrs with the saving passion of His Son.
We are all called in some way to suffer with Christ, and die with Him, so as to rise to new life with Him (see Rom 6:2-14; 8:17; 2 Cor 4:10). All of us share in the cross of Christ, so as also to share in His resurrected glory. If this seems unfair, remember God offered us paradise.
But Adam and Eve (and all of us have ratified their choice) wanted a better deal where they would call the shots. Welcome to the “better deal.” So God makes use of suffering and death to bring greater life, if we have faith!