I recently had this question from a past student in one of our science communication classes and thought the answer might be a useful tip for others as well.
I'm resizing my conceptual diagram and the stroke thicknesses are not shrinking along with everything else. I know there is a simple way to fix it. I remember the problem coming up during the class, but I can't remember exactly how to fix it. I've tried using Illustrator help, but it's kinda useless. Can you refresh my memory of how to do that? I have illustrator 11 now.
In Illustrator go to Edit>Preferences>General and check the 'Scale Strokes and Effects' checkbox.