What we are discussing here is the question of God's "sovereignty," his authority over everything. Friedrich Nietzsche, the famous skeptic of the late 1800s, tells how he came to the conclusion early in his life that if we are to thank God for the good things that happen to us, we have to give him credit for the bad as well.  Coming to this conclusion was part of the unravelling of his faith.
But his idea is nothing new. This is the standard view, for example, of the bulk of the Old Testament--"The LORD gave and the LORD has taken away; may the name of the LORD be praised" (Job 1:21). Similarly, some Christian traditions like the Calvinist one tend to see God orchestrating even the details of our lives. A very popular Christian book a few years back, The Purpose Driven Life, presented a view of life that saw God's hand in almost everything that happens to you in life, God teaching you lessons and helping you grow in almost every detail. 
However, I as someone from the Wesleyan tradition do not accept this view. For one thing, we also find passages in Scripture like James 1:13, which says no one should think that God tempts them to do wrong. "For God cannot be tempted by evil, nor does he tempt anyone." This verse gets at the heart of Nietzsche's complaint. If God is truly in control of the world, then he must also have control of the evil that happens in the world.
But there is a difference between God's directive will and God's permissive will, whether he directly causes everything that happens or in many cases only allows them to happen. Yes, God is sovereign. If he is king, all-knowing, and all-powerful, then he must ultimately be in control of everything. The question is if he has created a world with some degree of freedom or if he micro-manages everything directly.
Some of those who take a very directive view argue that if God would allow someone to disagree with him or violate his will, then he would not truly be sovereign. But this argument seems rather unsophisticated. Could not a parent intentionally allow a child experience the consequences of disobedience so that the child can learn, for the growth of the child? In fact, this is a much more mature and sophisticated picture of God, rather than one that almost sees him flying off the handle in rage every time someone disobeys him or worse--as someone who causes people to disobey him so he can how his greatness at blasting them out of the water? In short, is God not sovereign enough to choose to allow people to disagree with him?
This is the position I take as a Christian and that I will advocate in the rest of this chapter. Romans 9 does have some "naughty verses" for this point of view, but every theological point of view has its passages to deal with, and the Calvinist view seems to create a picture of God that is not only incoherent, but makes him at least borderline evil, indeed almost Satanic. It does not fit with the picture of God elsewhere and, in the end, seems more a particular kind of "language game" in Paul that we should not take completely literally.
Yes, for God to be sovereign he must "sign off" on everything that happens. But it does not mean he must orchestrate and plan everything that happens. The best suggested answer to the "problem of evil," although it is not perfect, is that a world in which God gives people the freedom to make good and bad moral choices is a better world than one in which they cannot help but do good. God thus has created a world where people can disobey him for a greater good--and a world where we find evil and pain.
 Beyond Good and Evil