Sometimes I just Shake My Head

As I've written before, there are things in the Bible that I just don't get.  I ran across another one of them today. 

One of the criticisms of Islam is that it is not accepting of other religions at all.  If you are a Christian in a Muslim country you are often persecuted.  If you convert from Islam to another religion you receive a death sentence.  If you are a Christian or another religion and you proselytize in a Muslim country you are risking your life. 

And we call this barbaric and unenlightened.  Imagine my surprise when I ran across this passage in my reading today.

Numbers 25:16-18(NKJV)
¹⁶Then the Lord spoke to Moses, saying: 
¹⁷“Harass the Midianites, and attack them; 
¹⁸for they harassed you with their schemes by which they seduced you in the matter of Peor and in the matter of Cozbi, the daughter of a leader of Midian, their sister, who was killed in the day of the plague because of Peor.”

Here we have a passage where God tells Moses to harass and attack the Midianites for basically the same thing.  I don't get it.