Not every ship in your armada is going to be the "big guns, blow apart the enemy" sort of ship. There are going to be those ships that simply make all your other ships more "big guns, blow apart the enemy." That's what you get with the Phoenix Home. You're not going to be scratching too many kills into its hull, but it will make sure your other ships are making those shots.
Not to say that the ship doesn't have any guns. 4 dice at the front arc isn't bad, but mostly you're going to be assigning crew and upgrades to the ship. Making it the Phoenix Home gives you more crew as well as allows you to have extra command tokens assigned to it. Those tokens can help your ship survive as well as command the different squadrons around it.