The same question could be asked during WWI or WWII when millions died. the same question could be asked during Pol Pots massacres or during the Moslem attacks on Thais, Filipines, Indians etc.
The same question has been asked ever since righteous Job sat on a dungheap scraping his scabs with a potsherd. It is a mystery that may not have a satisfying "human-scale" answer. I have watched a friend turn his back on God and the church and contentedly die in his sins over this question. That is why I take it very, very seriously, seriously enough to be a PITA on this thread. Scripture DOES speak to the matter. Here is some of what it says:
God IS in control of ALL things, even bad ones:
Amos 3:6 Shall there be evil in a city, and the LORD hath not done it?
But in his soveriegn power He uses evil for good:
Genesis 50:20 But as for you, ye thought evil against me; but God meant it unto good, to bring to pass, as it is this day, to save much people alive.
Yes indeed, He uses all things for good:
Romans 8:28 And we know that all things work together for good to them that love God, to them who are the called according to his purpose.
Evil has no power over His children, even though they may be slain. God has a larger purpose that we may not see:
Romans 8:36-37 As it is written, For thy sake we are killed all the day long; we are accounted as sheep for the slaughter. Nay, in all these things we are more than conquerors through him that loved us.
In case that is not enough for us, we can reflect on God's answer to poor Job. God is greater than us, and some things are manifestly His business:
Job 38:4 Where wast thou when I laid the foundations of the earth? declare, if thou hast understanding.
This crude effort just scratches the surface. I am aware that it is not satisfying. Better men than I have not been able to untagle the web. It is better just to trust God and be content.