But how does a ship, most likely auto piloting in orbit, give you benefits on land?

Well you equip the ship so it would have a character buff on it. If your looking for the rationale it would be something like: "The BOULDER class spaceship is designed with the fighter in mind, with extra cargo room for ammunition." If your going to pay 10k glimmer for a rare or above ship I feel it should be justified by something more then a different design/color that your only seeing at loading.

I feel you on paying that much glimmer for something. The one thing I think we aren't taking into account is how much glimmer we will attain. I maxed out 3 characters in the alpha, bought a number of weapons and armor, as well as 3 ships, and I still had like 12k glimmer left over

Oh very true, not to mention it seems like most of the high end gear will either be found or bought with faction marks not glimmer. So you'll probably have extra to burn. It's a minor nitpick really just sits in the back of my head wondering why my expensive rare/legend ship would be essentially as useful as the starter one. Though I have seen odd rumors/posts about specific ships needed for other planets. If you needed an uncommon ship to get to mars and a rare to Venus THAT would be a nice touch and also validate ships having rarity.