If you ask me, this doesn't make sense. If Clark doesn't want Lois, then he runs away from her and generally pushes her away and refuses to tell her about himself. That makes sense. But if he truly does want her, the he shouldn't do these things to her, should he? It doesn't make sense.
It does if you add in his insecurities regarding Lois, cultivated during the first season and the Luthor fiasco.
Firstly, he's afraid how she'll react--if she's really angry, he could lose even his friendship with her, which is very important to him even without the feelings he has for her.
Second, he's never told
anyone, so he's not sure how to go about it.
And third, their jobs/lives are so busy that he's been having trouble even
making the time to tell her properly--"Lois, I'm Superman" isn't something that is appropriate to be blurted out as you're flying off to a rescue, after all (and Jimmy/Perry interruptus doesn't help either).
This isn't to say that he's not hurting Lois--on the contrary, I know she's very hurt. But there are two sides to the issue, and Clark's feelings shouldn't be dismissed as unimportant or not as worthy of consideration as Lois's.
And then, if you get into meta-fandom (using a gaming term--a la meta-gaming--to describe this, since I don't know if there's an appropriate fandom term), you could just say, "The writers of the show weren't allowed to have Lois know yet, so they made Clark give all those excuses and it added some pretty good conflict to the plotlines anyway."
