I would argue that while Superman was never threatened physically he certainally was emotionally...that seemed to be the entire crux that Singer was going for with his version of Superman. What would happen to the world and to Superman if he had been gone for a period of time? Clark returns to find his world entirely thrown for a loop and like any human has a tough time attempting to adjust to the changes. The woman he loves--who thinks he abandoned her--has moved on with another man--a good man--and has a son (remember he doesn't know that its his when he intially comes back) his own mother has moved on from the death of her husband (she's seeing Ben Hubbard in the novel). All these changes had a profound effect on Clark (him spying on Lois and Richard with his x-ray vision). Then you have Lex obtaining more Kryptonite and creating an entire continent with it, essentially attempting to "steal" or corrupt Superman's legacy, that of his homewolrd. These are all emotional threats to Clark...there was no need for physical threats in this movie. I agree though this needs to change in the next one.