Interesting, difficult and fundamental question. (warning: I’m NOT a theologian, just an ordinary Catholic)
So, some passages in the Bible, apparently inspired by God, would seem to indicate that God condones cruelty.
And how do we define cruelty? It seems to boil down to the experience of suffering and death, especially when dealt by the hand of another intelligent being.
How could a good God allow this, or in this circumstance, even condone it? The atheist thinks, a truly good God could never allow this, so there must be no God. Eat, drink, play, and hope to die of a coronary in your sleep.
But what if God does exist? What if, in spite of our best efforts to discredit the Bible and the Church, the sea really was parted, or water did become wine, or water really was walked upon, or lame people really were cured, or dead people really were brought back to life? What if we then had to deal with the a reality of the existence of God, who obviously also allows suffering and death to exist? There are one of two possibilities, either God is unconcerned about our natural aversion to pain and fear of death, or maybe, just maybe, contrary to our sense of what is “good” (eg. comfort, security), there is an important, even crucial, purpose for suffering and death that is completely understood by God alone, that brings about an ultimate good.
And that’s not just Christians making up explanations to explain suffering. Jesus, in his life, showed us. The Church, in the last 2000 years, has been trying to better understand it. A lot of people in his time couldn’t handle it, why should anything be different now?