I can't say for sure it will be just time for you as I'm not a doctor so can only say for me things improved over time.
I hadn't thought of it is a phobia, perhaps it is though.
I could never tolerate open heights, cliff edges, tops of tall buildings, walking over high bridges. I would experience an almost overwhelming sensation I would fall. I remember when very young this could be so strong I would actually 'freeze'.
I guess it is natural enough this surfaced during my early flying lessons. In the end I think it was just trust in the fact the aeroplane wasn't about to fall out of the sky and I wasn't about to fall out of it. But it did take quite a long time before I could say I was really comfortable with the concept. So glide approaches, stalling, flying in rough conditions, go-arounds all built up a picture in my mind that aeroplanes are happiest in the air and things were just fine.
I'm sure I've read somewhere that fear of open heights is more common in pilots than the general population. Sorry I don't have a reference for where I came across that, but I'm sure this won't be the first or last thread on PPruNe on the subject.
I know one thing that helped me was discussing the problem with my instructor, he admitted the same fear of open heights and that helped me a lot to convince myself flying simply wasn't the same thing.
