There are different causes of suffering, much of it is caused by sin. It is often horrific, senseless, and certainly not the will of God. Rather, it stems from the abuse of free will by created beings (angels or men) and results in judgment by God.

To understand why God PERMITS such things to happen, I recommend this article - Why Does God Allow Suffering?  Below I will deal with a different kind of suffering, the kind that is CAUSED directly by God

The Bible is full of references where God causes hardship, suffering, sickness, and even death. Atheists and skeptics often use these verses to attack and ridicule Christians. Some don't know how to respond, so they ignore or downplay these sections of the Bible. Such passages seem irreconcilable with a God of love, but denial doesn't make them go away.

Others think they need to be an " apologist " for God and go through considerable theological gymnastics, trying to defend their " warm and fuzzy " view of God. I think it's much easier to simply accept what scripture says and take God at his word.

For instance, consider the flood. Suffering and death on a worldwide scale, but God didn't just allow it, he says he caused it (Gen. 6:17). The whole human race, even the children, and babies wiped out except for one family.

How about burning the people of Sodom and Gomorrah (Gen. 19:24-25)? Before you say that was Old Testament-style justice, note that Peter says it is an example of what is going to happen again , but this time on a massive scale (2 Peter 2:6). 

How about when God commanded Israel to slaughter entire people groups - including the women, children, and animals (1 Sam. 15:3). There is a word for that - genocide. 

What about the plagues in Egypt? Old Testament again, but plagues from God will come again as revelation states, causing suffering, sickness, and death. It's an inconvenient truth for some, but the "slain of the LORD will be from one end of the earth to the other " (Jeremiah 25:33). Isaiah calls it his " strange act " (Isaiah 28:21). Strange behavior indeed for a God of love -  or is it ? 

Some reason that those people deserve it, they are evil, they are enemies (even the babies). Some proclaim that GOD would never do (or allow) anything bad to happen to a righteous person, only the wicked. The book of Job shows that to be an immature view, not in line with Scripture, and incompatible with our existential reality. In Job's case, it was actually because he was right with God, that God allowed Satan to bring calamity, loss, sickness, and even the death of his children . Job suffered greatly in the test  to prove his faith.

Our view is myopic, we don't see the " big picture " of what God is accomplishing in us, let alone in the realm of the angels. Having lost their position in heaven, the fallen angels have been confined here to the earth, but they are still active and at war. The book of Job lifts the curtain for a " peek " into what goes on behind the scenes. God has reasons for what he does (or allows), his actions only make sense in light of this revelation. 

God makes the point (Job 38-40) that our minds are finite, our lifespans are limited, our perspective is narrow, his ways are above our ways and past finding out - we must trust and obey, even though we may not understand his actions or motives. There is an unseen world around us, and as Paul says we wrestle not against flesh and blood . Much of what occurs in our reality, must be framed in the context of a larger reality that is beyond the "ken" of man . 

Theologians and philosophers frame this issue in terms of antecedent will versus consequent will. God would prefer us to live in a garden of Eden, wallowing in eternal bliss. However, he created us with free will and we chose a path of sin and rebellion. He responds with a plan of salvation that involves faith, repentance, discipline, and a process of sanctification.

Some teachers deny that God would ever bring affliction, or that suffering can be good for the soul. They promise only health, wealth, sunshine, and lollipops, but what does the word of God say?

Psalm 119:67 " Before I was afflicted I went astray, but now I obey your word."

Hebrews 12:10-11 "No discipline seems pleasant at the time, but painful. Later on, however, it produces a harvest of righteousness and peace for those who have been trained by it."

Consider God's discipline. A small boy may not understand why their Father disciplines them and forces them to eat right and exercise, or doesn't allow them to go somewhere with their friends. Although the boy can't understand and resents his Father's discipline, it doesn't mean that his Father doesn't love him - correctly understood , it is evidence that he does love him. 

We tend to forget that in response to the fall, God's desire is not for us to be spoiled and lavished with creature comforts. That's what the natural man wants but is it what God wants for us? He wants us to develop tried and tested faith, and proven character. 

He cursed the ground for man's sake because in our existential sufferings, we learn lessons the ease of the Garden of Eden couldn't teach us. Show me someone who has had ease, comfort, prosperity, and health all their life, and I'll show you someone whose self-indulgence has forged the spiritual mettle of a marshmallow . 

It's trials and tribulations that develop perseverance and proven character, not ease and luxury. Seek ye first the Kingdom of God and his righteousness, and all these things will be added unto you. Most of us want the worldly treasures added on, but in seeking the Kingdom of God, also expect persecution, trials, tribulations, and tests - we are told to expect them .

1 Peter 4:12-13: " Beloved, think it not strange concerning the fiery trial which is to try you, as though some strange thing happened unto you...  

All scripture is God-breathed and useful for teaching and correcting, for training in righteousness, but " head knowledge " is not enough. God wants us to " live " our faith, to prove it by what we do , in good times and bad . He wants us to develop tried and tested faith that can stand strong in the face of adversity .

All the trees are green in summer, but when the cold blasts of winter come, only the evergreens are not left naked and ashamed . Anyone can be a "fair-weather Christian" but when the storms of life come, only those who have truly built on the ROCK will still be standing.

The important thing to remember is that the trials and tribulations do not negate God's love, they prove it . He disciplines all those he LOVES - it's what some people term " tough love" .  He cursed the ground for our sake, he prunes us, he purges us, he refines us, but all for our ultimate good. The trials come only for a season and exist for a reason. God is growing us up, sanctifying us, striving with us, purifying us. 

Job's faith was tested and he was a better man because of it. The fact that God gave back double what was taken from him, was just a bonus to the real benefit - faith tried in the furnace of affliction .  

Isa. 48:10 Behold, I have refined you , but not as silver; I have chosen you in the furnace of affliction .  

This is a HARD TEACHING and some refuse to accept it. Some prefer smooth and pleasant words that " tickle their ears ". They heap up teachers who will paint a rosy picture, and give them a cosmic " Santa Claus " in place of God, who will give them everything they want, accept every behavior, and demand nothing difficult from them. 

Don't get me wrong, I'm not against comfort, abundance, and provision. I'm not saying we should live in squalor, suffer the indignities of poverty, accept ill health, or go live on a mountaintop. God wants to bless our finances, our health, our relationships, our circumstances. However, there is a greater blessing he is trying to produce in us, and we tend to stifle it with our worldly lusts.

For instance, God may want to bless you financially, but not if it's just going to corrupt you, or diminish your dependence on him. There is a blessing that brings all other blessings in its train, and God will go to great lengths to ensure you don't miss it. Like Job, he may deprive you of your worldly wealth to test your faith, or to lead you to an even greater blessing. 

James 2:5 Listen, my beloved brethren: did not God choose the poor of this world to be rich in faith and heirs of the kingdom which He promised to those who love Him?

It is true that God is the giver of every good gift. It's our perception of what is good for us, and how God should provide these gifts, that may be lacking. Faith is good, but it needs to be refined in the furnace of affliction. Growth is good, but it comes with pruning. Correction is good, but it comes with discipline. Perseverance is good, but it comes through trials and tribulations. Promotion is good, but it is preceded by tests. 

Physical health is good, but like the child who is upset when his Father forces him to eat vegetables (instead of junk food) and walk (not be driven) to the bus stop, we want spiritual health without the hardships that help produce it. 

Consider the butterfly, it must go through a mighty and heartrending struggle to escape from its cocoon. If you open the cocoon to make it easier, it will never be strong enough to fly. In the same way, we need the struggles and hardships of our lives to strengthen us spiritually. Lack of faith traps us in a cocoon of helplessness, but our struggles strengthen us so that we can one day soar with spiritual power. 

This is the place of ultimate blessing, that God would have us obtain. Like a refiner of silver, he holds us to the fire until he sees himself reflected in us. Then, when the dross is purged away, we are truly blessed and our passage through the flame seems but a light affliction, compared to the glory wrought in us—true riches, eternal blessings, pleasures at his right hand forevermore. The worldly treasures men seek, cannot compare.

For more study, here are a few articles from other Christian authors, which express some of the same concepts:

http://www.gotquestions.org/innocent-suffer.html

http://deeptruths.com/letters/sin_suffering.html

http://ericcarp.blogspot.ca/2007/04/question-4-does-god-cause-or-al...

http://bible.org/article/why-there-suffering