Though I probably should have qualified this somewhat. For one, with other makes, there are some automatic four-speed trannies with variable yada that can do as well as or better than manual five-speeds.
The bigger point to me is that it's worth checking the MPG for both the auto and manual versions of a particular model and year before just assuming the manual tranny will do better than the auto.
Lastly, as others are saying and MPG aside, I think manual transmissions tend to be cheaper to maintain and are less prone to breakdown.