Automatics also tend to have a heavier transmission. Any extra weight can add to reduced mileage. While I don't see this as much on modern cars, I *have* noticed that the automatics seem to go through brakes faster, which is likely due to a combination of having to brake more while stopping/stopped (transmission pulling forward instead of in neutral like many manuals) and because most people don't gear down on a slope in an auto like they would in a manual.
My main reason is control. My last auto always felt like the car wanted to drive me as soon as I took pressure off the brake. On varying road conditions, being able to pop the clutch has saved my bacon a few times. The more common situation is when I'm just starting to accelerate and push pressure on the gas, and something/somebody darts in front of my car. It's faster to pop the clutch and cease acceleration than release the gas and then brake. This has worked well when some Darwin-award-nonimee racing down a heavy slope on a skateboard (and/or often black clothes) at night runs a red when I'm starting to proceed through a green.