While most airport security lines will make you remove all of your electronics from your bags when you put them through security, not all of them do. It's always a gamble: will you have to remove the laptop or not? It's such a hassle to take apart your perfectly packed bag just to remove the laptop, only to have to put it back in again afterward. This can all be prevented with a special laptop bag.
If you don't want a special bag just for your laptop or your electronics, you can at least get a special pocket that makes it easier to remove and less affects the other items in your bag.