If a Spaceship is merely a way for the characters to get about, then having a Patron provide one, or the GM providing one as the common 'package' for everyone is perfectly reasonable.
That does not mean that wanting to treat a Spaceship as a piece of equipment (like a sword, or a horse) for which the PC needs to pay (points and/or cash) isn't a perfectly valid and reasonable option - for which our rules (GURPS) should be able to provide us with an answer. Dismissing this option in favour or just giving them one is not very helpful.
Treating Spaceships like Cars is also not a particularly relevant argument. I can't think of a mainstream fiction setting where everyone of Average wealth owns a spaceship; A 'flyer' or 'speeder' maybe.
Spaceships are more equivalent to Planes or Yachts (larger ones)
Private shuttles might be the equivalent of helicopters, small planes or small boats, but they are still not owned by everyone.
The 'What Cost of Living Gets You' box on page 266 of Basic:Characters puts owning a small yacht into Status 3 (which is basically Very Wealthy), a private light aircraft as Status 4 (basically Filthy Rich) and an executive jet as Status 5 (basically Multimillionaire 1)!
The problem with simply using Wealth to buy a spaceship is they are expensive - not particularly surprising, and Signature Gear doesn't really help either.
I would use PK's
Wealth and Signature Gear House Rules, and if a Characters spaceship is basically their home, I would have no problem with using the 80% of Starting Wealth to cover this.
In settings like Traveller, Star Wars or Firefly, where Spaceships are very common, I see no problem with simple applying a divisor to the costs. 10% of the sort of cost from a GURPS Spaceships design would make a 'tramp freighter' or small scout vessel a reasonable point purchase.
Using the 'Cheap and Used Ships' options from GURPS Spaceships 2, p27/28 is also an option. You can adjust the divisors/percentages (cheap as 20%, very cheap as 10% for instance) as above. These options have the added advantage of the ship requiring extra maintenance, which keeps the characters occupied.
The Supers/Headquarters rules suggested by the_matrix_walker are also a reasonable option if the Spaceships is more than just something provided by the GM, but not really personal equipment. The spaceship costs someone points (so it's not a freebie, and means something for the characters to look after), without it being a significant portion of their character points total.