I know that hero ships are moderately tough at the beginning but I imagine that by the time you reach mid to end game like other small ships they can be wiped out fairly easily by an opponent's larger ships. Can you get your hero to pilot a behemoth or a capital ship of some kind instead to keep them safer? Or put them on a ship class that stays as far as it can from battle?

That's not the case, due to several factors. In the end game

• you get high-tier defense modules, that multiply your Hero ship effective HP 4 to 6 times, because small ships have smaller hull weakness then large ones;

• your Hero ship is probably leveled up enough to have several times more base HP due to experience;

• hero ship usually is not a priority target.

Also don't forget that hero ship is, basically, essential. It will respawn upon destruction immediately after battle if your fleet survived, or after Hero healed up if your fleet was destroyed.

There is no more risk of losing hero ship in end game, then early on.

I try to make sure they are grouped in a flotilla with larger ships, but honestly, once the hero & fleet starts to level up, the only thing that can pose a threat (assuming relatively equal fleetsize) is a higher level enemy hero.  Even midgame and engame fleets will flee or turn to scrap before your onslaught if you've put some skill points into fleet offense & defense and won a few battles (pirates are great for this).

It also helps to re-fit their ships with better armor and weapons when you make it back to a friendly system, but I honestly forget to do that quite often and the hero ship still does fine.