It won't hurt and could save you shaking the snot out of your motor. I have seen a bumpy road cause damage to hood latches etc.
If the route you travel is super bad (logging road into a "secret back lake" etc) it's best to simply remove the motor and put in the trunk of your or back of your truck.
The motor is way way back there (think of a teeter totter with your hitch as the center and your motor out on one of the seats) - every little bump is amplified where it's located.
So, with a 9.9 (75lbs 2 stroke, 100 lbs 4 stroke) it's not so much the transom you are needing to save, it's more the motor itself..