I think I might be able to understand where Lois is coming from, but have to agree she is confusing Clark.
However, on the other hand, he has not even tried to confront her on that front. While Lois may be assuming too much that Clark understands what is going on, I would also say that Clark should vocalize his worries more.
Any misunderstanding occuring is just as much Clark's fault as Lois'.
