At least your thinking about it, which is more than I can say for myself when I was your age.
Basically if you were to do maths and physics at A-Level followed by an engineering degree at university then there is no doubt that would help towards your ambition to become a pilot.
However there is no point doing maths, physics etc and getting a D and an E or something which would not allow you to go to university. You have to strike a balance, if you despise maths at GCSE then perhaps thats not the best option. You'd be letting yourself in for a miserable couple of years, perhaps. Maybe doing physics without the maths would be a good idea, replacing it with a subject you are more interested in.