Does the question who are you taller than in your family sound natural? For example:
Your dad is the tallest in your family. Who are you taller than in your family?
What I am trying to ask who in your family is shorter than you.
What I am trying to ask [is] 'who in your family is shorter than you?'
That is exactly how most people would express it. Who are you taller than? is not idiomatic English, though it might be used by a child or in very informal speech.