I generally only pilot up to destroyer class ships. Anything larger is generally mostly turrets, so my flying it isn't as useful.
I usually fly a wolf, with 2(4) reaper torpedos, and try to use them at point blank range to kill enemy ships in one or two hits. Generally, I find that to be more effective use of my time. Capital ships, positioning isn't as important, and they tend to have turrets which do most of the work. The only significant advantage is the stat boost, which is no longer exclusively player's domain.
Sometimes, I use a Sunder, with a Pulse energy cannon thinggie (Rapid fire, limited ammo), but the AI can do that almost as well.