Why they should be balanced for all ships? As well there might be rule saying: no small ships would survive encounter with capital ship.
Just for enjoyability reasons, mostly. It wouldn't be very fun if you were basically forced to fly a large ship to survive near a capital ship. Small ships are already weak, there's really no reason to make capital ships especially good against them.
My ideal scenario is that Capital Ships have three layers of active defense. At the smallest level, fighters, which mainly deal with enemy fighters/small ships. At the next level, spray turrets, which do lots of damage but have a wide spread and turn slowly enough they have a hard time tracking smaller, faster ships, but which are capable of tracking medium ships, unless they put in a lot of effort to dodging.
Lastly, the capital weapons, which turn VERY slowly and fire huge, slow plasma rounds, slow enough they're dodgeable by even medium ships, but which cause extreme damage to either large player ships or enemy capital ships.
Oh, and lastly give them some pretty high Armor Hardness to make them especially resistant to small weapons.
So you've got small ships, which are largely ineffective at actually damaging the capital ship, but which are also hard enough to hit, the capital ship mostly leaves that duty to the fighters. Medium ships, capable of damaging the capital ship, but forced to do so defensively, reducing their DPS. And lastly, Large ships, with the weapon size and raw DPS to heavily damage capital ships, but which need all their defenses to tank the capital-class weapons, and if they also get attacked by the other defenses, are quickly overwhelmed.
Ideally, this would make all levels of ship size relatively equally important. The smalls need to go in and take out the fighters, so the mediums can move in and distract the medium turrets, so the Larges can move in and do the actual damage.
Yeah, that's a lot, but IMO capital ships really should be the 'boss monster' of human PVE. Right now they're honestly a lot easier than an Independent Captain. They should be seriously challenging, and give rewards to match.