Fighters could be good for taking out ship subsystems.
Example: Bada$$ enemy battleship approaching a squadron of your frigates and cruisers. What are YOU gonna do about it, if the ship gets in range it will tear you apart because a) it is bigger than you

it is meaner than you c) it is faster than you and d) You're in a gravity well unable to jump away...what do you do?
Answer: Send bombers to disable enemy ships engines
PROBLEM: Bombers destroyed
>think< >think< >wipe sweat from brow< come on the ship is getting closer, almost in range >still thinking< AHA!
Split the fighter squadron in two, task one half with taking down enemy fighters while the other half make hit and run attacks at the enemy battleship, hopefully taking out its engines.
Now your small ships can make hit and run manouvres at it, getting in, firing, legging it, the come about, fire, leg it again. Lather, rinse, repeat.