First of all you need to differentiate between phobia and natural fear. Phobia is a disordered that requires appropriate treatment. Natural fear is an inhibition that is meant to keep you from falling from dangerous heights. Sometimes inhibitions are a good thing (Chris already stated that).
If you feel the need to overcome the fear you can try get used to altidudes. You should not overdo it and for some things (e. g. rappeling) you should find someone to teach you properly to stay save.