One of the problems that has been a thorn in the side of most theologians is the problem of evil. They have no way to explain the existence of evil, since according to them God is benevolent, omniscient, and omnipotent. The argument itself basically points out that the very existence of evil, is contradictory to the attributes of the biblical God.
My own take on this argument is simple: when you think about the many inexplicable occurrences that we experience in life, such as death, rapes, murders, birth defects etc. It is easier to explain them when you take God out of the equation. There is for instance a perfectly scientific and sound explanation for birth defects, as opposed to trying to say that the child was born that way because it was God's way of testing the faith of the parents etc.
I call the act of trying to rationalize the existence of God, trying to make sense of nonsense. Christians remind me of that kids learning game where you have to fit certain pieces into a box with various shape cut outs. No matter how much you try you cannot fit a square piece into a circle. But by trying to rationalize the existence of their god this way, they are doing exactly that.
Ancient man was very superstitious and to this day even with all of the knowledge and understanding that we have gained about the world we live in, there are still many who refuse to let go of ancient superstitions. I personally count the existence of God or gods in general as superstitious and mythological in nature.
When you remove the concept of God out of life's troubles and hardships natural disasters, and whatever other calamity you can think of, then you can see them for what they are: natural occurrences. When you come to the realization that life is nothing more than a continuous string of random occurrences, then you will see the world with clarity.