They make you take it out because no one travels just with a laptop in its own bag. Generally people jam as much crap into their bag as humanly possible. Then you throw a laptop on top of everything making it pretty hard to see what the heck anything is in the bag. Thus they make you take it out and run it through separately. Plus its hard enough trying to see whats in a laptop without all the extra cables and books and stuff on top.
From my understanding that is the point of a "X-ray friendly case/sleeve", Nothing goes above or below the laptop. (no pockets in the sleeve)
http://www.tsa.gov/press/happenings/simplifying_laptop_bag_procedures.shtm