Speaking as an xbox player I generally use the stick on-line in sim, for a few reasons.
1)Looking around on the pad is really awkward (on xbox, no aviator control scheme on pads)
2)Because the stick is much bigger it's much easier to be gentle. I can keep the sensitivity higher without stalling than I can on the pad.
3)Thottle control feels much finer and under control. You know how much power your putting on without looking in the corner.
4)It makes me feel cool

I get my avi's on and leather coat and everything and start talking all "Jolly what pip pip. I say, it does appear they're shooting at us and shit". Just kidding....but not really