Coke,
In the US if you are flying along on an IFR flight plan, then you don't have to worry about getting permission to fly through various control zones (airspace Class B through D). It is up to the radar facility to contact the tower and point you out and get permission for you to fly through their airspace. It works the same way when flying VFR being worked by a radar facility.
If you are just tooling along on your own then it is strictly up to you to announce yourself, and in my opinion it is a very good idea to do so if you are over flying below 4000 feet, or if the field is known to have crazy people jumping out of airplanes.
I am curious if the procedures are similar in the UK.
Safety is a two way street,
Mike