It's not about an angry, vengeful God as much as a totally depraved creation. Humanity was evil and vile, and God got rid of it. He saved Noah and his family because they were good and what God wanted from his creation.
Nebulous, I was thinking of comparing with Islam and Judaism; glad someone agrees! Wondering whether the angry, vengeful God would be going too far? That is the sort of question year 6 will ask, though.
Polly, I need to work out my own LO; part of my problem. What would be appropriate to y6? I agree with the 'misunderstood' part of your post; not really all about cuddly animals going in two by two.
Treat it as a legend, look at the actual meaning of 40 days and nights as a period of time. Check what the known world was at that time for the people of the Middle east, and the words and imagery associated with God at the time. Concept of God as an angry, destructive force who will end the world if not appeased. Then redemption. Compare the story with Nu in the Qur'an Look at other flood myths from other areas.
For reasons too complicated to explain, I will be teaching the story of Noah's ark to Y5/6 next term. Obviously, I will have to approach it is a far more complex manner than the normal KS1 activities. Has anyone any ideas for an interesting take on the story at y6 level? I am particularly interested in RE ideas; I know that there are lots of great cross-curricular things to do with the story