You know, it's not like the Kryptonians were so perfect. They had wars. They have a ton of evil villains in the Phantom Zone. They arrogantly stuck to their erroneous beliefs - even when their best scientist was telling them otherwise - and let their planet get destroyed.
Kryptonians aren't monolithically good - or evil - and neither are humans. Superman is a
person, regardless of his planet of origin. Kryptonians were people. Earthlings are people. If Jor-El asks, "Are humans worth saving?", it seems to me that his son's response should be, "Well, was Krypton worth trying to save?"
Kal-El was brought up on Earth, has a human wife and a half-human son. It's his home now. It's got good people and bad people on it. I think it's a little late in the game to be provoking an existential crisis by pointing out that some of them do bad things. he knows that, and it seems to be true of most planets we see.
Superman's helping people who need help, protecting people threatened by dangers bigger than they can handle. Any doctor or fire fighter or Coast Guard officer does the same; Superman just has greater powers to do it with. I never got the impression that he thinks of himself as a god, come to judge humanity for their sins before deciding whether they're "worth saving," or to "save humanity" by making them all Good. I hope he rejects the whole premise of Jor-El's question outright, rather than try to prove "but there's good in them!"
I also hope that's not Jor-El. But that's just me.