The recoil not only jerks your shoulder back, but the shoulder motion also jerks your neck and head rather abruptly.
You didn't note if you were shooting offhand or off a bench. I find that the felt recoil from many calibers (especially larger ones) to be much more significant than firing offhand. This is because added rigidity from being seated and braced by the bench, though the discomfort is mostly just in the shoulder pocket.
Is your gun ported?
While your shoulder/back is "jerked" abruptly and may pull on your neck and hence pull your head, the jerk to the head should not be significant. Your shoulder, back and neck should have absorbed most of the recoi before the head is affected.
Note that in the following vids, the heads of the shooters really aren't jerked very much at all.
Here is a little kid shooting the .450 offhand.
http://www.youtube.com/watch?v=Fjhfjon_G88
Shooting off the bench...
http://www.youtube.com/watch?v=ZNNmk58aqJw
Now see this lady shooting. Her posture and mounting of the gun are wrong. Instead of leaning into the gun to help control recoil, she leans back and away from the gun. That position often causes folks to have to stand rigidly in order to hold the gun and maintain her backwards lean. As a result, the shoulder/back and neck fail to absorb very much recoil and so her head does get abruptly jerked.
http://www.youtube.com/watch?v=SR3hhOybQzI
This is not about noise, my earmuffs are very effective noise reducers.
As noted by johnwilliamson062, the shockwave produced during fireing can be bothersome or even painful. He was off to the side of the Barrett and so was explosed to alot of the shockwave. The shooter of the Barrett receives the least amount of the shockwave as the shooter is sort of in a shockwave shadow behind the gun. This should go for shooting rifles in general.
He also noted cheek weld. If you haven't mounted your gun properly, the recoil pulse can be transmitted through the stock to your cheekbone or side of the head and cause discomfort.
Having good hearing protection really only protects your hearing via the ears, but the shockwave can be felt elsewhere, including your head, so the issue certainly can be related to noise in the form of the shockwave.
I have found a couple of times where I had blocked sinuses or a sinus infection that the shockwave produced impacted my sinuses and producing a headache. Just a thought.
If the little kid in the first video can handle the recoil without his head getting abruptly moved around, you should be able to handle the recoil as well.