The episode "World's Finest" has some disturbing implications about Lois's taste in men. "The Late Mr. Kent" makes it clear that Clark Kent is who he is, and that Superman is just what he can do. Similarly, the Batman Beyond episode "Shriek" makes it clear that Batman is his true self, not Bruce Wayne. To quote Bruce: "She likes Bruce Wayne, and she likes Superman. It's the other two guys she's not crazy about." Is she really that shallow?
According to the creators, it's only Batman she really doesn't like, so make of that what you will.
When you think of Jor-El's plan to save Krypton, it's downward chilling and terrifyng: put everyone in the Phantom Zone and once Jor-El travelled to Earth, he release his people. Two words: Alien Invasion.