Lana did not like Clark being secret, but even she admitted thats part of the mystery of Clark Kent. He would not be who he is if he did not have some mystery to him. And the "Visage" episode at the end, when she found out Whitney was dead, she said that she didn't care about his secrets, that she never wants to loose him and he is one of the only good things in her life. Lana was going to go on a date with him after that episode, but Clark screwed things over, because Pete had the parasite in him, and used the red kryptonite to control him. Chloe was hurt, but Chloe got infected too, and Lana saw Chloe made out with Clark. Then shit happened between them again, and things went back to the way they were. Even when Clark apoligized with the rose, she threw it out
I know I would have been mad too, but Clark had no control over it. Not like they were really boyfriend and girlfriend either, but obviously Lana would have went for him regardless of Chloe's feelings.
That is all.