That’s difficult to explain, I don’t think you can really translate it. Was machst du? means What are you doing?, and the so turns it into a more general question. If you ask this question you want to know what the other person does in his job or what he/her does as a hobby.
Was machst du? would be asked if someone is now at the moment doing something and you want to know what it is, and Was machst du? so is asked if you want to know what the other person does normally in everyday life as a profession or hobby.