Surely not everyone killed in the flood was evil. What about the children? For a religion that is supposed to support life, this story seems rather blood-thirsty.
I don't have the best answer for this. Frankly, natural disasters are one of the more difficult hurdles that I have to jump in my religion. Still, I posit the following (and please remember that I am not a theologian nor a geologist):
The world has survived many extinction-level calamities (us humans causing the largest of them all in number of species ended). Humans have feared the omen of a comet in the sky (attributed to some level of calamity in nearly every culture of the world). At some point in our past, a comet appeared in the sky, growing steadily bigger as it approaches and is captured by the Earth. God warns His people of the danger, but only Noah listens. The rest of the people deny the threat; some of them throwing "end of the world" parties. God warns that their preparations need to include species of animal and bird rather than merely the creation of a life raft to hold people and a few supplies. This event will require a massive rebuilding. Only Noah and his family prepare. Some people perhaps half-heartedly imitate Noah's plan, but nothing near the scale that he attempts.
As the extra pull of the heavenly body asserts massive tidal pressures on the Earth (pulling the water through the gates of the ground), people begin their panic, still not listening to God. They loot, rape, and murder as people so often do in the face of looming disaster. Noah makes his final preparations and closes the ark. The comet finally ends its orbit and crashes into an ocean. Massive tsunami cross over the Earth. Hurricane level storms fill the atmosphere. The world is covered in water.
Noah's ride is not an easy one, but his preparations allow him to survive. By listening to God's warning, Noah saved our species from a species-killing event. Over time, the warning would be against the sinfulness of those who did not listen to God. While true, the story of Noah is more powerful to me because it shows not a mass-murdering God, but a God who warned us and showed us how to save ourselves from a world-ending event, and the man who listened.