I have also noticed this.....I am running 10.1 on an Acer Travelmate 4101.
It runs hotter than in Windows....seemingly around the area where the memory modules are installed (!).
The Travelmate is a Centrino, so I usually manually set the speedstep down to the lowest value as it still runs great- this keeps it cool enough to stop the fan coming on ..... but still hotter than under windows.
I do wonder if it is not the CPU that is getting hotter, but some other component.....gfx card/memory maybe???
It does seem to be fine though running at full speed.....it just gets a bit hot.....but I have left it on for hours like that with no adverse effect.
There is a link to an Ubunto related forum that might be of some interest to you:
Hope this helps!