I've taken mine just in a backpack, which is useful when you go into town.
If I haul a laptop again, I may opt in getting an el cheapo chromebook, and have a little piece of mind of not hauling my pricey mac. You can get them for like $50 used.
Sea to Summit makes a nice laptop sleeve for a little padding:
http://www.seatosummit.com/product/?item=Travelling+%26trade%3B+Light+Laptop+Sleeve&o1=0&o2=0&o3=488-32wrap that in a drybag, and you're good for weatherproofing.
But, yeah - I feel it more secure in my pack, that's on my back in a crash situation.