Yes, that bothered me too (especially in flute parts where the fermata frequently went right on top of the note), so I manually dragged and dropped it up a little higher each time I did it, but I got tired of doing that, so I went in search of the answer. I found it following these steps (using MuseScore 0.9.5)...

1. ) Select "Style"
2. ) Select "Edit Style"
3. ) Click "Articulations, Ornaments"
4. ) Select "ufermata" (up fermata)
5. ) Above that, increase the "Articulation - note stem distance". It's set at 0.50sp. I found that increasing it to 1.50sp is perfect for me, but if you want them a different height, you can fiddle with the amount to get just what you want.
6. ) Click "Ok"

Now all fermatas that you place should be higher. I assume you could do the same thing for fermatas that appear under the note by selecting "dfermata" and increasing the same setting, but I put all my fermatas on top no matter which way the stem goes, so it works for me.