I agree with Christopher. Batman is an orphan, Spider-man is an orphan and lost his uncle Ben, Tony Stark's father died young in the cinematic version, James Bond is an orphan, Bourne has no family (that he remembers), Wolverine has no family, Captain America's family are presumably dead, Harry Potter is an orphan, the Starks lost their father and mother in GOT, Kirk's dad and Spock's mum died in ST'09.
The whole losing a parent thing seems to have become such a cliche of late. It might have been nice to keep Jonathan around in the MOS-verse.
Makes me wonder if the creative minds have all some sort of father issues.