I've been meaning to write an article on this topic for a while, but here is the jist.
When you scan, most likely the scanning software is going to take a stab at adjusting the contrast, etc.. anyways for you unless you specifically say no. I don't see anything wrong with "scanning flat" and adjusting to taste with a human input vs. letting the computer do it automatically for you. I think many people miss the fact that their images re being "manipulated" automatically when they scan them, even if they don't have a say in it. I think the traditional photographer more then anyone appreciates the importance of having control at as many steps as possible.