I think there are mods that enable better hulls for hero ships. Otherwise you can have bigger ships drawing the fire away from small hulls with certain modules. And don't forget Heros are revived at the end of a fight if their fleet survives.

I feel like the hero ship has much bigger chances to be instakilled when there's no medium hulls in the fleet that could take fire for them. Hero ship is supposed to be relegated to support role once the ships in fleet "grow". Shame the slots on it don't reflect that fact as well as the hero-only modules that you can discover suggest.

The Unique Planet quest line give some very strong Hero mods if you do the “colonize a Unique within x turns” choice.  Scent of Victory module buffs your morale boost by 50%, which is massive.  Pretty sure it stacks with the morale buff from the Team Spirit Tactic card you can find by exploring curiosities.  The other two modules you can get depending on your unique planet are: an increased fleet xp module and a repair fleet per turn module.  The Scent of Victory module seems strongest by far, but the other choices sure aren’t bad.  XP for ships doesn’t matter when you build at Legendary rank lategame.  Scent is always obscene; you roll one or two lanes and the last enemy lane gets torn apart like a Furby in a woodchipper.  To keep your Hero safe, make a tank hull for each lane.  Coordinators with an AM Lenser and flak and Carriers with a Blast Effect Battery draw all the hate I’ve seen apart from bombers.  Squadrons like to go for Hero ships.  Gotta mount one or two flak slugs on the Hero ship to counter those.

Thank you people for the enlightenment !