Was it fair for God to flood the world in the days of Noah?

So when sceptics want an example of times that God was cruel and unfair and went way overboard with dishing out punishments, what better example is there than the time he drowned every living thing on the planet with the exception of one family and a selection of animals?
Doubly offensive to them is that Christians often use this one as a favourite children's story.

So the basic set up that everyone knows is that Noah and his family were the only people following God, and the rest of the world had got nasty and were doing their own thing. So God wanted to start over and just keep the good stuff.
This is actually a great foreshadowing to the end times, and is even referred to by New Testament writers as a comparison. Just like how in the Flood, water washed away the wickedness and made things good and new again, in the end times the same thing will be accomplished with holy fire (2 Peter 3:6-7). '1 Peter 3:29-30' tells us that baptism is a symbol which corresponds to Noah's Flood, which again is making the point that it is all about becoming reconciled with God, and being made new.

But the point sceptics try to make is that this mass drowning was an extremely harsh judgement.
Let's look at the connection Noah's Flood has to the end times. In the final judgement, those who do not choose God will be destroyed. So, Noah's Flood, being a precursor to that, shows us these people as examples of that. They turned away from God and were destroyed so that the good and faithful could live in a better world without them.
As detailed in my article on God's plan, God's goal is to create a perfect world. There is no room in a perfect world for sinners.