I think you got all good answers.
I used to commute on the Honda 130 miles round trip daily. Really old Bates hardbags. Carried my old Dell laptop all the time. No problems.
On the Sprint I've travelled with my Macbook. For work it is usually in my flight pack strapped to the seat; but I've had it in the hardbags, too. I've had it in a Seal Line padded case, and without. So far, no problems.
Of course, if you want to get really fancy and drop some bucks, I think Aerostich used to sell a laptop travel case made to attach directly to your luggage rack. Bit much for me. I'll just keep shoving it in my pack.