I know.
Fighters are a powerful weapon throughout Proportions' tech tree. It's difficult to get ship-based weapons that can lay waste to them like in the unmodded game, although Fire Control Centers can let bases and weapon platforms do a very good job. However ships can cary their own fighters, and if your fighters are set to target their fighters, their fighters will probably die if they try to concentrate on your ships.
That's all pretty much an intentional situation, and is pretty much in line with modern air/naval combat and much sci-fi as well (cap ships without fighter cover versus fighter/bombers are in big trouble).
Ideally, I'd have time to go re-work some of it, though.
PvK