Sorry if this seems harsh, but the cabin crew really doesn't care if your laptop gets damaged - that's not their primary concern. What they care about is the overall safety of the flight, which means ensuring your laptop (and every other piece of carry-on luggage) is stowed securely so that in the event of an emergency – turbulence, crash, etc. – it does not become a projectile flying around the cabin with the potential to injure someone.
To that end, the safest way to carry your laptop from an aviation perspective is exactly the way the cabin crew instructed you to: Either secure it in the overhead compartment, or place it under the seat in front of you.
Holding the device in your lap is generally not an option because in an emergency you may not be able to hold on to it, nor would you want to be sitting at an awkward angle "holding it by the handle" to keep it off the floor if the plane suddenly encountered turbulence, as your head would very quickly meet the back of the seat in front of you - likely in the vicinity of the tray-table.
Typically neoprene laptop sleeves should provide adequate protection for flying with your laptop, but clearly you are not the typical situation (either your flight was unusually rough or your laptop is unusually sensitive). If you are concerned about damage I would suggest purchasing a laptop bag with more substantial padding - these are bulkier than the neoprene "sleeve" style cases, but provide substantially more protection and are better suited to flying. In addition they're usually big enough to hold travel essentials (at the very least a change of underwear/socks and any personal medications) as well.
If you can't get a more substantial bag before your next flight the bubble wrap idea is a good one, but make sure you can unwrap the laptop quickly when going through airport security - a wad of bubble wrap with some electronic bits inside may attract some extra attention.