I always assumed that it was because the main threat the seatbelts are trying to deal with were bad turbulence.
In such a scenario, if the plan rapidly drops and you're sat, the 2-point belt at the waist will keep you on your seat. If you're lying flat and you have the same belt you'll probably just sandwich your head against your knees or worse - especially if you're lying on your side or back!
I never checked to see if there was any validity to my thoughts though.
I wouldn't think it is really 'acceleration', just mass continuing at the same speed, when the aircraft and seat surrounding it might stop or change direction more suddenly. Relative speed change, but deceleration or change of aircraft speed, not acceleration of your head?