because they look for specific markers on the y-chromosome (or mitochondrial DNA). More on edit if the project's FAQ has anything enlightening to add.
Edit: Boy, the FAQ wasn't overly helpful; I have a feeling it was written before anybody asked any questions, frequently or otherwise. Anyway, the closest it comes to bearing on the question is here
https://www3.nationalgeographic.com/genographic/faqs_results.html#Q16 where they said this: 16. What if my results show an entirely different location, country, or place than what I know to be true about my early ancestors?
Your results reveal your deep ancestry along a single line of direct descent (paternal or maternal) and show the migration paths your ancestors followed thousands of years ago. The migratory route is one part of your history and does not preclude what you already know to be true about your more recent genealogical past. It has no bearing on your cultural identity, ethnic heritage, or nationality of the more recent historical past. Your individual results may confirm your expectations of what you believe your deep ancestry to be, or you may be surprised to learn a new story about your genetic background. You will not receive a percentage breakdown of your genetic background by ethnicity, race, or geographic origin. Nor will you receive confirmation of an association with a particular tribe or indigenous group. This is not a genealogy study. You will not learn about your great-grandparents or other recent relatives, and your DNA trail will not necessarily lead to your present-day location. Rather, your results will reveal the anthropological story of your direct maternal or paternal ancestors—where they lived and how they migrated around the world many thousands of years ago.
... which is pretty much what you and I said already. Sorry I can't be any more helpful.