When i ride with a laptop I keep the laptop in a soft padded laptop bag and then stuff it into a pannier which I leave on the bike.
That way it is double-protected and I have a reasonable way to carry my laptop around at my destination.
At times i have also ridden with my laptop and laptop bag stuffed into a large Marmot daypack. Again, for the double protection. But them I did most of my serious bike commuting in the harsh climates of Seattle and Juneau before moving to Texas.