I had a similar thing a while ago. Commute approx fortnightly AMS-MAN-AMS and ended up thinking too much about why I was flying at in an aluminium tube, doing 450mph+ over the ground, at an altitude above which no human being can survive for more than a very short period. Started getting quite freaked out by this thought and feeling really quite claustrophobic in planes.
My only solution to this was to get stuck into a good book to take my mind off it! I also find reading can be quite settling if I happen to feel slightly uneasy or disorientated during some bumps/turns, particularly at night if I have no horizontal reference visible to me.
I also tend to feel more comfortable in larger types (320/737) than smaller a/c like the EMB145/135, so maybe if you can choose an operator who flies larger a/c that might help too?
Good luck, just don't give it too much thought - its all in the head
