I've noticed this before... like in the mission where the Aquaetine need to be evacuated from the nebula and a Moloch jumps in, I usually stay behind (with the disabled Moloch...I save big things for the last) trying to destroy it but even with all of my wingmen shooting at it it's not blowing up! 1% and not exploding!!!
It would look more realistic just making the fighters completely useless against Cap ships, only being able to destroy turrets and subsystems.
The only non cap ship that should be able to destroy a cap ship is the bomber with it's bombs ,from common sense point of view of course.