Some of the hardest parts of the Bible to deal with are God's seemingly harshest judgments against entire cities, people groups, and, during the flood, even the entire human race save the 8 on the ark. Why were God's judgments so harsh? How can a good God wreak so much destruction upon those who bear His image?
In truth, it is because those who were judged were not bearing His image. These people were impenitent sinners, corrupted to the core, and very much deserving of their punishments. The real question isn't why did God destroy them, but why didn't He destroy everyone else?
According to Peter, those who received the wrath of God on Earth serve as examples. They were God's way of saying "this is how passionate I am in my hatred of sin, this is what will happen to you if you don't repent". The flood is especially presented in such a way. It doesn't just show what happens to the ungodly, but ultimately illustrates the Gospel. Those who step onto the ark (i.e. put their faith in Jesus) are saved. Those who don't perish with the rest of the ungodly world.
If we are to succeed in our mission as Christians, we need to understand this concept. We need to stop looking at how horrible God's judgments seem from our human perspective, and instead look at what they tell us about how horrible our sin is from God's perspective. Let's be honest here: The whole point of punishment is to be detestable. Those who receive punishment deserve punishment. Those who see that punishment seek to not receive it. The problem, of course, being that we already deserve it. The place where the sinning angels are kept, that's where we deserve to be chained. The flood that covered the ancient world, we deserve to drown in. The ashes to which Sodom and Gomorrah were reduced to, we deserve to be reduced to. Every single one of us, believer or not, has done something against God to merit that kind of punishment from Him.
And so yes, we should be disturbed by these things. And we should be disturbed by the fate that awaits those who cross into His divine courtroom with sins left to account for. These things should disturb us, because they are disturbing. But not because we serve a scary God. Because we serve a just God, but also, more importantly, a loving God. While we see our God is more than capable of executing the most terrifying judgments upon the ungodly, we also see a judgment He was more pleased to execute (Isaiah 53:10): The bruising of His only Son. The judgment faced by the Lord Jesus Christ was brutal, so much so that the word "excruciating" was made up in reference to its practice. In the flesh, our God was beaten mercilessly, so much so that He barely looked human. He had a crown of thorns thrust into His head, and as He bled, He hung from splintered wood by nails hammered through His wrist and His feet. And why? He was innocent! The only human being ever to walk the earth who did not rebel against God. The only human being who did not deserve death.
The reason is "simple", and well documented throughout His book. The punishment He received, He received for you. He died so that the horrors faced by Sodom and Gomorrah, by the rebellious angels, by Noah's flood, will never befall you. When you die and face God in judgment, He will know every one of your sins. You've got nothing to hide from Him, He knows every thought, word and deed. But then He can look at the cross and say that the penalty for every one of those sins has been paid. So now you get to be "on the ark", you're going to land on the mountain, and step out into a brave new world. An eternal, sinless world where death itself has been banished, all bought for you by His own blood, and received if you will only repent and believe. That is why God destroyed certain cities.