In this context, the sovereignty of God implies the goodness of God's rule. But how can we know that God is good?
Some point to the beauty of the world, or the complexity of designs in creation as evidences of God's wisdom, power and goodness. However, we also know that the world is full of diseases, disabilities, accidents, malfunctions, parasites, decay, pain, suffering, and violence -- and above all, death. To whom do we attribute these evils?
Bare theism has no answer to this. Young-earth creationism attributes all of these evils to the Fall of Adam and Eve, prior to which they did not exist. But this implies that there was no death before the Fall, and the fossil evidence (not to mention the massive evidence of a long time-scale) does not support this.
"To the question, how is the world to be conceived as a good world in spite of the evil within it, the biblical answer is simply, 'in Christ'. The evidence that God loves the world, and cares for mankind, is the Cross of Christ. There he has shown full proof of his love. 'For God so loved the world that he gave his only begotten Son ...' (John 3:16).... That is how much God cares for his creation -- much, much more than any cosmic clockmaker or any Principle of Causality could conceivably express. Consistent with the agency of creation in the Old Testament, the New Testament speaks of Christ as the Word of God and the Wisdom of God, in whom, through whom and by whom all things were made."
-- James Houston, I Believe in the Creator, p. 126