This is a very difficult and complex matter, and it is hard to see one's way forward.
Surely as a matter of faith we must confess that God is not the author of evil, which then leads us to make the distinction between primary and secondary causality, between those events that God determines and those acts that God permits.
And yet equally surely our reflection cannot stop at this point. When calamity and disaster occur, we immediately cry out to God, "Why?" Deep in our hearts we understand that precisely because God is creator and sustaining cause of everything, precisely because nothing occurs apart from his will, he bears responsibility, at least indirectly. Nor can we simply blame Satan, for Satan is not the maker of heaven and earth: God has not relinquished control of his universe over to a created being.
Evils committed by human beings can at least be explained as actions chosen by free agents, but how do we explain tsunamis, earthquakes, tornadoes, cancer, and bubonic plague?
There are no easy answers, yet it seems to me that the gospel bids us to believe that somehow God is in control and will bring all things to the good. But I also agree with David Benison Hart that natural evil is also profoundly contrary to God's will:
I do not believe we Christians are obliged -- or even allowed -- to look upon the devastation visited upon the coasts of the Indian Ocean and to console ourselves with vacuous cant about the mysterious course taken by God’s goodness in this world, or to assure others that some ultimate meaning or purpose resides in so much misery. Ours is, after all, a religion of salvation; our faith is in a God who has come to rescue His creation from the absurdity of sin and the emptiness of death, and so we are permitted to hate these things with a perfect hatred. For while Christ takes the suffering of his creatures up into his own, it is not because he or they had need of suffering, but because he would not abandon his creatures to the grave. And while we know that the victory over evil and death has been won, we know also that it is a victory yet to come, and that creation therefore, as Paul says, groans in expectation of the glory that will one day be revealed. Until then, the world remains a place of struggle between light and darkness, truth and falsehood, life and death; and, in such a world, our portion is charity.
As for comfort, when we seek it, I can imagine none greater than the happy knowledge that when I see the death of a child I do not see the face of God, but the face of His enemy. It is not a faith that would necessarily satisfy Ivan Karamazov, but neither is it one that his arguments can defeat: for it has set us free from optimism, and taught us hope instead. We can rejoice that we are saved not through the immanent mechanisms of history and nature, but by grace; that God will not unite all of history’s many strands in one great synthesis, but will judge much of history false and damnable; that He will not simply reveal the sublime logic of fallen nature, but will strike off the fetters in which creation languishes; and that, rather than showing us how the tears of a small girl suffering in the dark were necessary for the building of the Kingdom, He will instead raise her up and wipe away all tears from her eyes -- and there shall be no more death, nor sorrow, nor crying, nor any more pain, for the former things will have passed away, and He that sits upon the throne will say, “Behold, I make all things new.”
Without this hope, how can we live?