I thought I was the only one with this fear!
When I explain to people that I hate heights, yet have a PPL, they all think I am crazy. I too think it is more of a fear of falling than the actual height. I am quite happy buzzing around at 3000ft inside a closed cockpit yet i recently did one of those "Go-Ape"high rope courses and found it hard to climb up a 50ft tree!
I also climbed Snowdon a month ago and there was one point near the top where, after climbing 800m of the total 1000 or so, I nearly had to turn back. A 10m stretch consisting of a 6m wide ledge with 800m drop either side To say I !!!!! myself is an understatement. I literally had to run across that section. I thought that completing it may cure my fear, or atleast ease it but it didn't!
Being in control when flying definatley makes a difference. I used to dread stalls (fear of falling out of the sky!) when my instructor was in control yet when I do them i'm fine. Its purely because I am in control and can stop the falling if I need to. I even told my examiner of my fear and he was very understanding. Still had to stall etc but he didn't dwell on the subject for any longer than necessary!
Stick with the flying. Once you get more into it and feel more comfortable and understand what is going on in greater detail, you will be fine.