I agree, and I believe it is a combination of two things:
1) Clark was taught to be polite and sometimes he doesn't realize that there are times when you have to forget your manners and do what needs to be done.
2) Clark was also taught to hide his powers, his strength. His parents meant in a physical way, but I think that eventually he got in the habit of hiding his strength of mind as well.
When you are taught something so consistently from such an early age, it becomes a permanent part of your psyche. So it's Martha and Jonathan's fault.
(Of course, it really the fault of TPTB on the show, because they wanted to ratchet up the tension to keep viewers.)
Another good example of him not being assertive enough was when Lois/Wanda convinced him that she wanted to go with Lex. Yeah, right! Clark should have bodily removed her from the scene. There would have been some nasty consequences but nothing could be as bad as letting her go with Lex.
