Ehh, there are many explanations that do make sense (within theology, anyways). It's really everyone's assumption that "omnibenevolent" somehow magically means he wouldn't allow any harm or ill feelings, which... is a very silly premise to begin with. Many people also remove God's own free will by somehow thinking omnipotence mixed in means he must do certain things.

I don't believe in the BS most religions teach, or basically all of them if you take their teachings as a whole, but the absolutism in some of the dismissals get just as silly. Many teach about human free will, which immediately tells you that God can choose not to do things in the first place, let alone all the, "mysterious ways" crap.

Also, a funnier direct explanation could be that all that BS about humans being special and that other animals are just chattel for us to take care of and bla bla... What if God has been talking to some other species the whole time and we're just hearing bits of the convo? I'd laugh my ass off if those sorts of religions were largely correct but turns out it's like dust mites that are the chosen ones, and we're just their giant dust cows.