Why does God permit the persecution of innocents?
God created man good, in his image and likeness (Gen. 1:26-27). Our first parents willfully decided to rebel against God, thereby sinning and welcoming death and other negative implications, including suffering, into man’s earthly existence (see CCC 396ff).
The practice of free will by some can indeed entail the persecution of the innocent, whether ancient Israel under the oppressive reign of Egypt for more than 400 years, Christians and others in the Holy Land by imperialist Muslims (which precipitated the Crusades), and the killing of millions of Jews and others during Hitler’s reign.
And yet God does not leave us amidst such persecution. He sent his eternal Son to redeem and save us (see John 3:16-17). In addition, by his sacrifice of Calvary, Jesus shows how suffering can be redemptive. Similarly, though he does not actively will our sufferings, he can allow them so as to bring about a greater good (see Rom. 8:28), including the right to serve the persecuted (see 1 Cor. 12:12-26, Matt. 25:31-46) and, ultimately, assist foster our own ultimate eternal salvation.
Further, as noted above, the persecution of the innocent can lead in their unjust killing, as it did for the Holy Innocents when Herod sought to seek and destroy the Christ Child (Matt. 2:16-18). And yet death did not have the last word in the case of the Holy Innocents, nor will it for others unjustly persecuted unto death. God is in control and will ultimately and gloriously vindicate those unjustly persecuted.