I think the point is simple...
no fighter in theory should have enough firepower to completely take down (and I mean to reduce in pieces) a capship of almost any class, even a (single) bomber shouldn't be able to.
You would need wings and wings of bombers to seriously damage/destroy a capship.
This should be true unless you hit (by luck or purpose) a critical spot, if there is any. Even in this case you shouldn't be able to destroy a capship, and if it is possible, then it is the capship that suffer of a very bad design.
A battle between fleets should be a battle from distance between capships, using their huge firepower against each other.
With interceptors to attack enemy bombers and torpedos, and maybe to attack the weapons of enemy capships, to reduce their firepower, and their critical subsystems, to be deployed as fast as possible as reserves when/where needed.
With bombers, making torpedoes runs from safe distances, to project and increase the firepower of their own capships, to destroy critical subsystems.
With tactical ships, like ultra fast/light bombers to make sneak attacks, stealth bombers/fighters, etc etc for alternative stragies.
With fighters, to cover the bombers, to gain flight supremacy and to destroy enemy interceptors.
With antifighter weapons on capships to destroy enemy interceptors before they reduce the firepower or they cause too damages, and with antitorpedoes weapons to intercept enemy bombs.
You still should be able to destroy a capship with your alone fighter, but it would be almost impossible, you will have to be both a god between the pilots and an extremely lucky man. And still you would die 9 times on 10
But, on the other hand, this will require a real AI for all the computer controlled ships, starting from the capships.
Without a decent AI, the bombers are ineffective (look at the ravan mission), and the capships just sit there, firing at whatever comes in range. In this situation, if you really want to see capships going down, you just need to give more chanches to destroy a capship to the player.
Not to mention that it is fun to destory enemy big ships, it makes you feel better, althought it makes a game more arcade than a semirealistic simulator.
Btw there are worse situations than those in FS2.
I remember in xwa I took down in the same mission, alone, at max level of difficulty, something like 5 Stardestroyers with all their fighter complement, using a ship that should be just a transport:/