Let me try to clarify a little bit. When I said the difference between a personal and commercial license is the ability to charge, I'm talking about the real world. In a gaming context I can easily imagine it being the same.
I'm right there with you in wanting the pilot to be a part of the team, but you have to be realistic about it. If he's the only one that's paying for gas, port fees, registration, maintenance (and even upgrades) then he's going to be unhappy with not having money to spend on fun like everyone else. Even if he's not, the party is going to end up getting stranded because he won't always have enough/make enough to cover upkeep.
Really, imagine the conversations. Heck, have your players sit down and do it. Introduce a brand new pilot. Unless he's completely shirking his responsibility, that is, not even remotely playing in character (and that is bad role-playing), that character is going to be just like Han in ANH: Here's my rate. If things go well and he stays, upkeep has to be dealt with and the only fair way to do it is for everyone to contribute equally. It's not even hard to do it.
Now, if you, as a GM, don't want to worry about finances, that's different. It's like playing D&D and no one ever buys food. Some groups just don't track the piddly stuff and I'm cool with that. But the questions was posed: Who pays for it? So it's important to some people. For those people, there's only one way to do it. It's not about keeping a player at the table, but keeping the character in the group. The characters have to have motivation. Screwing each other over, whether it's stiffing on the tab or conspiring to steal a ship, might be fun for the players, but it absolutely destroys the characters working together.
I'll try to keep these relatively short.
I was playing an old school Ranger in AD&D with a new group. This group was a bunch of power gamers. Tons of high power spells and magic items. Kill one monster after another. Not particularly interesting. I never got to participate in any fighting because they were such a well-oiled machine that the big beastie was always dead before it was my turn. Well, they messed up and I had a chance. I had a bead on a dragon, arrow sighted, called shot to the eyeball. I rolled two natural 20s in a row (the DM required a second one) for the hit, then rolled max damage (complete with absurd bonuses that this group had given me because they felt I was under-powered). Killed the dragon and they were ticked. Shortly after we broke for dinner. The guy who invited me took me aside to let me know that the group felt that I was a power gamer and they didn't want me playing any more. I rolled a grand total of three dice in five hours. I literally laughed out loud and said okay and left.
With another group I was playing a WEG Jedi in ANH era. I asked if it was okay and the GM said sure, no problem. First time I went to use my lightsaber he informed me that it had been stolen. Apparently it happened the day before. Apparently I never noticed being bumped into in a non-busy place. I couldn't find supplies to build a new one even if I had known how (apparently I had forgotten how I did it the first time). The group wouldn't help me find it, either immediately or after the mission. So my character went off on his own to find it, which resulted in him leaving the party.
Same group, I had a WEG tramp freighter captain. Same sort of stuff we've been talking about here. I wasn't saying they had to pay me. I was saying they had to help with costs. They wouldn't and we got stranded on Nal Hutta. That is, I got stranded on Nal Hutta. I was back with the ship trying to get it working and then out of impound while they were off on a mission, and they went off-world. I took what was supposed to be a quick side mission for a little cash and a part and ended up never seeing the party again. A short while later I left the group.
"The party gets a ship" is just a bad rule if that's all there is. Someone has to own it (and it really shouldn't be a 120K ship, it should be 40K used, tops). If it's a benefactor/creditor of some sort that's cool, but it still comes down to one person owning it. I don't know about you guys, but I would never let a player start with a ship free and clear.
Dante, I don't know your gaming experiences, but here's some of mine. Games in high tech environments frequently start off with some players having expensive, high tech gear, including starships. It's generally understood that the character is not just now striking out on his own. Luke may have been 1st Level, but Han sure as heck was not. There's nothing ridiculous about it, and is really just an opportunity for adventure. Looks like you have a nice ship. Too bad you couldn't outrun that customs corvette and had to dump your cargo before they boarded you. Looks like the Hutts have put a bounty on you. Again. Or maybe you did lose the pink slip in a game of sabaac, but you decided to skedaddle before paying up, and now he's after you. There's lots to on out there.
That said, if "the party gets the ship" then "the party pays the upkeep." I don't know why this is so hard to understand.