I can think of lots of uses for manned small craft.
Space to space combat vs peer opposition is not one of them.
The rules allow me to mount a bay weapon that can destroy a small craft in a single hit at ranges beyond the small craft return fire range. Since I can maintain that distance then any squadron of fighters will be shot out of the sky before they can close.
Fighter vs. a ship with a bay weapon isn't really peer opposition though is it
Even so it is not necessarily a guaranteed win.
Let's take a Midu Agasham destroyer. It has a small particle bay, 6x Triple Missile Turrets, 8x triple Pulse Laser Turrets, 6x triple sand casters and 2 point defence batteries. It costs over MCr1800.
Lets fight it with Ultralight Fighters. In default configuration they cannot hurt you so they won't try it. To make them effective though you only need swap the pulse laser for a missile launcher loaded with 4 advanced missiles. It will cost you less than MCr7, so I can field over 260 of them.
We both have thrust 6 so I can stay at whatever range I want and so I can stay out of your pulse laser range. I can afford to expend quite a lot of thrust on evasive manoeuvres before you can close the range enough to start to threaten me with the pulse lasers. That assumes you do not expend any thrust of your own to evade. I might drift close enough that you can target with your particle bay after you have expended a total of 25 additional thrust. Even if I remain stationary that is 4 rounds. Since the basic space combat rules abstract the movement we can ignore the fact that I could choose to break into wings and attack from different vectors meaning that closing on one wing would distance you from another.
In round 1, you can only target 6 of the fighters. We will assume you also have advanced missiles If you fire a volley of 3 we can safely assume you will hit with at least one and can eliminate a fighter with every volley. You expend 18 missiles to do so. If you fire less missiles there is a good chance that you won't hit all 6, but you could extend the endurance of your turrets as otherwise you only have 20 rounds before your magazine is exhausted. The missiles do not arrive instantly though (7 rounds for Advanced missiles at Distant Range).
In round the fighters launch 260+ single missile salvos at the Destroyer.
At the end of the round each sensor op on the Destroyer gets a chance to destroy 1 salvo. It is not guaranteed, but with good sensor ops you can stack the deck. But how many good sensor ops and sensor stations does the ship have The default is 3.
Rinse and repeat for the next 3 rounds.
The fighters can now concentrate on not getting hit as they are now unarmed, they likely disperse so they cannot be hunted down en-masse but will remain close enough to monitor the situation.
In turn 7 the missiles arrive. The fighters can try sensor ops but it isn't their primary job so they will be unlikely to succeed so let's say you kill 6 fighters.
Lets say every Sensor Op on the Destroyer has a successful EW action every turn for the previous 6 turns and the Destroyer eliminated 18 salvos. Your point defence batteries eliminate another 2 and the pulse gunners might kill another 6. We'll even allow the pinnaces to take out another 2. That is still 230+ attacks to resolve. Any that succeed do 5d-4 damage. I can't see anything other than armour on the Destroyer that defeats missiles. These are conventional missiles so the nuclear dampers are irrelevant (you don't need nukes).
Rinse and repeat for the next 3 rounds.
At most 24 fighters have been destroyed (less than 10% attrition and pilots could probably eject just before the missile hits). The rest disperse and head for their various bases to re-arm and maybe have another go.
I can't see the destroyer surviving.
Now I haven't ever used the fleet action rules so I might be missing something there, but the above is my reasoning why I think fighters can be effective, are not automatically suicide ships and can afford and even benefit from human pilots.
I am sure there are those that will argue that the Destroyer isn't the last word in capital ships, but then neither is the ultra light fighter particularly optimised.
You might argue that 288 fighters is ridiculous, but you could probably achieve the same effect with 50. You can get 30+ Heavy Fighters for the same cost as the Destroyer. It has a missile launcher by default and has a pulse laser as well so it could have a shot at point defence, and definitely EW. It also has impressive armour and a deeper magazine. With Thrust 9 it can afford to evade and still maintain distance. It is less likely that a single salvo of 3 missiles would be a guaranteed kill. Each kill would be a greater impact on the squadron though.