I had it late in my CPL training, and it worried me SH!TLESS (more for what my Father would think....) He knew, and I pushed myself, and overcame it. I love flying MUCH TO MUCH to let something psychological overcome me.
I wasn't so much a fear of flying, it was an intangible feeling in the bottom of your gut - a "WTF" feeling, something I am having trouble to even describe!
The way I overcame it was to fly solo A LOT, and make myself THINK about FLYING THE GOD DAMNED AEROPLANE - not what some instructor was thinking. I just AVIATED, and left the rest of mundanity and trivilaity behind.
What REALLY made me shine was doing aerobatics. I did over 60 hours in a DH-82 Tiger Moth (hence nick name!) - I even passed my 100th hour in that Tiger! Not only did I learn aerobatics, but I learnt what a lot of younger pilots these days do NOT learn - recovery from UNUSUAL circumstances - inverted, genuine spinning, approaching Vne etc (you could fly the Tiger at Vne, because it was an AERODYNAMIC Vne, not structural - in otherwords, the airframe has so much parasite drag, that it cannot go any faster!
Learning aerobatics not only instilled much needed confidence back in me, but it was a wake up call that BY GOD I LOVE FLYING!!!!!!!!
Sorry to have wandered off topic somewhat here, but in my opinion, there are certain areas of training SADLY and SORELY ommitted from training these days.