I think for a couple reasons:
1)you need the ground clearance - it's amazing how easy it easy to end up with the sump on the ground

2) it helps if the top of the bike is flat, giving you more room to move around. This leads to an overall higher bike.
You get used to after a while - besides, you are supposed to spend most of your time with your feet on the pegs... not on the ground!
;-)