But he is "one of them".
Sometimes I think the writers forget that a little baby was brought up by his foster parents, and his name is Clark Kent, and Clark is "one of them". That's the whole point.
There is something entirely wrong with Jor-El addressing an adult Kal-El (I have always hated the idea); and it is just bollocks that he would say to this grown man, "You are not one of them."
Are you implying that Richard Donner and Geoff Johns don't "get" Jor-El? Are you disagreeing with "Superman: The Movie"?

To be honest, I don't really like it either. But when Marlon Brando said those lines, there was something awesome about them. And I really like Jor-El's latest look. Having the movie dialogue appear in an actual comic book, though, does make it clear just how wrong it is for the traditional version of the character. It takes Superman's sense of alienation that increased all through the Bronze Age and brings it to an incredible new height that actually gives fodder to the Byrne Reboot argument.
For me that's a minor nit that's worth living with. I like the movie interpretation of the mythos as well as the comic book ones. I figure there are worse continuities that they could have chosen to use, the movie one has incredible elements.