There are a lot of different reasons why manual is best. Sometimes auto does a pretty fine job, but in certain lighting situations, manual is the only way to go. I just recently got back from a vacay to Florida, and while landscape photography is definitely NOT my strength, I got this pretty awesome photo on a beach in Key West.
ISO 2000, f/4.0, 13 second shutter (it was super windy, which is why the clouds and palm trees are moving)
This is what auto mode came up with when I turned the flash off:
And this is what auto mode came up with the flash on. (that shadow is from my very wide angle lens)