Car seats have become more and more advanced over the years with newer models having integrated side impact airbags. While side impact bags are important for side impacts, the most unprotected direction to protect from is the rear end. The mainstay of protection for the rear impact is the headrest. But if not positioned properly, the headrest offers little protection. In some cases, it might even accentuate the injury mechanism.
The first and most important aspect is the distance from the back of your head to the headrest. Your seat should not be reclined. While this might make it "cool" for cruising, it increases the distance from head to rest, making it useless for whiplash protection. Instead, maintain a more vertical stance, with your rest just touching the back of your head near the top.
The reason you want your headrest high is that your body may rise slightly during a rear-end collision. If your head rest is positioned too low, then the head may bend around it like a fulcrum, increasing the amount of trauma your neck experiences.
Another issue to consider with car seats is their position from the front seat airbag (often inside the steering wheel). You want to be at least one foot away from the steering wheel/airbag because it will deploy with dramatic force (approx. 200 mph). If you're too close you could receive chest and internal injuries form the airbag itself.
If you're aware that someone is not going to stop, it's best to brace yourself and have your head touching the rest and not turned. A head turned during impact can sustain in even more substantial ligament injuries.
Take the time to check the position of your seat and headrest the next time you get into the car. Are you far enough from the steering wheel? If not, then slide the seat backwards. Is the seat almost vertical? If not, check with a mechanic to see if an adjustment can be made to the seat. Is your headrest positioned high up so it's just touching the back of your head? If not, adjust it.