nogwart: Thanks again, crazy_dave! Your advise and link did help somewhat. I'm playing on easy. I do see the hull/shield percentage drop when attacking single fighters now. The mission I just played only had me fighting single fighters, not big ships, so I'll have to look for that the next time I'm going up against a big ship. My mission results showed 41% hit for my last mission, but I have no idea if that's good or crap. :) I suppose it's the "big ship" missions I'm having problems with because I don't really understand what I'm doing in them yet.
And, yes, I'm still using mouse and keyboard, and it's working out pretty well since I maxed my mouse sensitivity.
Anyway, sorry for ranting. I'm ok now and am moving on. :)
41% is really good against fighters. Generally I get in the thirties playing on medium/hard.
Against capital ships you want to target their subsystems - although some cruisers (smallest capital ships) have relatively weak hulls that you can take down with missiles or even primaries. There is one Shivan cruiser, the Lilith, with a ridiculously strong hull though - those are very unpleasant to deal with. Larger than cruisers (i.e. corvettes and destroyers) and you probably will target subsystems only (or ignore) unless you are in a bomber or a heavy fighter with powerful missiles/bombs and even then sometimes you'll only target subsystems like the sensor array or a particular turret.
There are some missions when you need to protect the larger ships agains enemy bombers (and of course their bombs). Those can be ... stressful, but you do get a lot of kills from enemy bombers. :) The best bet is to either use really powerful single missiles against the bombers far away, or the small rockets + primaries when up close and personal.