The problem of evil is a devastating argument against God - taken by many as an argument for atheism, and taken seriously by believers. The concept of natural evil is particularly hard to shake off, and for good reason too. While it's debatable that free will can explain what agents do to each other, how does one explain the devastation of an earthquake? Yet an earthquake is not inherently evil in itself, it's a consequence of living on the planet we do. And this is where I think there's a problem of indifference rather than one of evil.
The universe does what it does irrespective to the desires of humanity. while people can attribute floods to God's wrath or ponder the ultimate greater good that comes from such an event, the notion that the flood is just a flood is far more devastating emotionally. There's nothing to reconcile because there's nothing there. We could be wiped out tomorrow by an asteroid and the universe would continue without us. Natural evil might pose an apparent contradiction, but at least there's something there to be seemingly contradictory.