For me, it depends on the type of flying I'm doing. Usually, if I'm just cruising around with a trainer or glider, I use my thumbs(and sometimes not even on the sticks![X(] ), If I'm flying 3D, or warbird, or something I'm more "concerned" about, I end up using index&thumb.

It really is up to your personal preference, just like holding a pencil.

BTW, If your pressing down with your thumbs so hard that it bothers you or hurts your thumbs, then lighten up and relax. It only takes small movements to get your plane going where you want it to.