It seems to work okay from my perspective as well. While missiles are great at hitting small moving targets and making huge holes in systems, they don't penetrate armor very efficiently as their damage really does get split between all the armor blocks in radii working out from the point of impact. Cannons will penetrate armor more rapidly and leave small holes in it, but can't eat up systems as rapidly. Beams just seem to miss too damn much for players to use. I use them for ai craft only, since ai is server side and has better information to guide its shots, but when they do hit they deal damage to armor and systems beneath simultaneously, which means a beam system will hit up your systems even if it can't make a hull breach.
Now, with shipyards that can do repairs, we can field more armor-based craft that can handle a beating. They're going to be slower overall, but still...
And yes, individual fighters will never really, and shouldn't be expected to, be able to stand up to the guns of a large capital ship. Fighters get their value from numbers, coordination between them, and agility to avoid harm. But expect the first hit they take to take them out of action, even if not overheating, more often than not. Fighters should take advantage of weapons that let them repeatedly hit targets weakest points for the entire duration of their presence in its field of fire. If theyre a bomber that relies on hard hitting pulse combos, then hit and run tactics should be used. Don't wait in your opponents sphere of influence while your torpedo recycles, leave. Your goal is to be in range only long enough to deal damage and then leave, its your enemy who wants to keep your bomber squadron in range as long as possible in order to take out more than a handful every run so they can't be hit as hard next time. Beam weapons are probably great for fighters trying to disable larger ships' turrets, by damaging systems beneath the armor. You need only deal at least 50 damage to unarmored systems at depth, though that does rely on knowing the thickness of armor. Turrets probably won't have much more than a single layer on average though, their objective is to mount weaponry.
Admittedly, we have no coordination whatsoever between fighters because of the ai limitations. Fighters right now are either players willing to die a lot or disposable drones that can't really do anything useful because they're tactically retarded.