I've been mulling over an important idea over the past few weeks. It's stemmed from things I've seen written in several books over the years, by authors whose spiritual opinions I respect. I might be wrong in my interpretation of their words, but from what I understand, they have stated quite strongly that God does not cause suffering. He may use it, but not cause it. “[He] does not prefer and promote suffering and pain.” 
When I first read such statements, they seemed true. However, in light of recent events, I've had a hard time matching them up with my own experiences. Some suffering absolutely originates with evil—but I don’t think we can say that about all suffering. In the West, we tend to assign the label “evil” to anything we deem unpleasant. However, the Japanese view suffering as a neutral entity: not good or evil, but simply a part of life. This viewpoint seems to hold a substantial amount of truth when compared with my own experiences. I continued to puzzle over the conflict between these points of view.
Then, one day in devotions I read John 15:2, which says, “Every branch that bears fruit, He prunes it that it might bear more fruit.”
Would not a branch in the midst of being pruned feel that it is suffering? Would not the gardener be the cause of that suffering?
Peter and I recently had a discussion about superheroes. We talked about how the common perception is that superheroes protect people, battle injustice, and capture the bad guy. But Peter pointed out that “protecting people” isn't really the job of superheroes. They don't usually protect individuals. Usually, they fight to protect society as a whole. Sometimes, in fighting against the bad guys, superheroes might break a window or smash a car. The individual owners of the window and car may not have had their property protected, but the greater good is served. They are protected from oppression.
Superheroes sometimes do have special people that they individually protect. Peter pointed out, “We all want to be Lois Lane.”
As I thought about this—about our desire to all have our own personal Superman— I realized that the fulfillment of that desire would be self-defeating. Each of our own personal Supermen would probably end up hurting someone else in their quest to save us. The superhero’s quest must ultimately remain at a macro level in order to retain any kind of meaning.
Going back to the issue of pain, and whether God causes it, I can't help thinking that perhaps we Christians need to zoom out and look at this issue from the macro level too.
It's easy to say that God is kind, and therefore he cannot desire pain for us. He doesn't cause it.
But, as C.S. Lewis once pointed out, a God who is only kind could be responsible for unspeakable horrors. For example, if certain groups of people were suffering, would He just eradicate them to eliminate that suffering?
Does God's kindness cancel out His goodness? His love? I think not.
Just as a parent punishes a child, just as a gardener prunes a plant so that both grow in a healthy way, so God may cause suffering to accomplish a greater good.
A gentle nurse does not leave a bullet in her patient simply because she's run out of anaesthetic and the removal of the bullet will cause pain.
Gentleness and kindness cannot be allowed to overrule love or goodness.
There are many good things that can come from pain. I have seen them in my own life.
Job 2:10 says, "If we take happiness from God's hand, must we not take sorrow too?"
When we say that God does not cause pain, we partially disable ourselves from seeing what purpose He might have in it. And what joy can be ours when we see the smallest corner of His plan, and are able to gratefully affirm: “The plans of the Lord are altogether good and perfect!”
It is true that God does not take pleasure in our pain. Rather, His pleasure lies in the pruned plant that thrives and grows, bears fruit and waves its leaves in praise to its Gardner and Creator.
The Japanese say that suffering is an intrinsic part of life, and they are right. But so is joy—if we have only the eyes to see and hands to pluck its sweet and tender fruit.
 Brennen Manning, The Ragamuffin Gospel. p 5 of 17, chapter 4 of the ebook.