I hope this thread isn't too old to post to.. anyway, as a tip, something I observed while trying out the multiplayer servers.
As stated earlier PTA systems engage missles (though they don't do enough damage in time to kill the missle, of course that is what EMD is for.)
If your in a fighter (say an elite pilot, or an AE Commander out on a strike mission in an FC), and your going to engage a carrier or cruiser, normally their PTA's will just chew you up before you even get into range, or at least should, unless your so lucky to come in at a blind spot.
You can distract the PTA system with missles. To allow you time to get in close to hit with your guns.
Keep in mind this doesn't always work, mostly you have to be lucky that your target was moving when you activated hyperjump, so you don't end up on top of him when you come out of hyperspace, you need to be just outside of range.
You come out of hyperspace and go full throttle at your target, when you see your shields get their first brush (or as soon as you get nervous) fire a volley of missles (I fire a couple for good measure, but I suspect you only need one).
While your closing range feel free to just keep your guns firing maybe you'll get some lucky hits, you only really seem to get em good once your close enough to see their shields flare up with your shots, after you've knocked out their shields, and you've done a few shots into their hull, Hyperjump outta there, by then their PTAs are probably back on you, and you need to get out alive with your shields intact, because you need to go in for another run once your shields recharge..
If you stayed in their long enough to get into their hull/armor, its likely you hit some crititcal systems, you can probably finish them off with your next run.
My prefered fighter for this is the S24-Raven, I chose this because of it's high speed, as imho, the less time you spend closing range the better chance you have to survive. Though I have yet to try out all the other fighters fully.
BTW PTA's look really pretty when they aren't firing at you
And of course this should be the main reason your CC should have a fighter escort