My doctor said my ears are way too clean. is making the hair inside really thin. is that bad?

No, good: Every one secretes oily substance and sweeps out side ear canal and by regular cleaning , is cleared clean In some it drys out and becomes wax in ear .You don't have wax means you are keeping ear canals clean and maintaining good hygiene

Odd : Ears that are clean is EXCELLENT.!! Hair in ears is not a particular need. Just be careful how you clean ear canals -- that you do not damage ear drum etc.