Answers for Is there a specific reason that the letter Y is used as the symbol for the male chromosome and X is used for the female chromosome? Why not YY and XY?
This is an example of convention. Conventions are all around us in all science fields and even in our lives.
Perhaps that convention about the male chromosome is derived from its shape when condensed, smaller than the X chromosome, combined with the fact that Y is the next letter after X. If you find other explanations, please, comment here.