"The Midianite women mentioned in Numbers 31 purposefully seduced the Israelite men into committing idolatry and child sacrifice and other horrific things. So any woman who had done that was put to death, that is merely justice done. The virgin women had not committed that crime, so they were spared.

And it wasn't for sex slavery or whatever you and other skeptics think. What else did you want the Israelites to do, leave thousands of young girls in the middle of the desert with no family or ability to care for themselves? They would have died or been forced into prostitution or something like that. So God commanded the Israelites to accept them into their nation, and they become Israelites themselves.
As for why the males being killed

We have an example in Haman the Agagite, the villain of the Book of Esther, who was descended from the line of the Amelikites, whom the Lord ordered Saul to wipe out completely.

If Saul had done what he was told, this all could have been avoided. I know our brains cannot comprehend or see God's plans, but we have to trust in faith that every one of those male children of Midian would have grown up to be evil, and would have caused great harm and evil to themselves, and to others, especially the Israelites. So God had them killed.

Another thing to note is our general belief that children and babies are precious to the Lord, and our hope is that when they die, they go straight up to be with him. So killing the children will have been the greater good as well, sparing them a life of sin and the burden of following the same wicked paths their parents walked, sending them up to the Lord instead.

Finally, it should be noted that the text I think specifically says boys, so we cannot be sure that babies or male children below a certain age weren't spared. Perhaps it was just the boys who already had been exposed and initiated to the barbaric and evil ways of their people, and therefore too far gone, who were killed, and the rest of the males were spared as well. In fact, we hear about Midianites in later chapters of the Bible, so actually we can assume that some were in fact spared."