Greg Mortenson's story as told in Three Cups of Tea is significant for several reasons, and these reasons translate into its primary themes. This is certainly not an exhaustive list, but these ideas should get you started:
Perseverance in the face of adversity - Greg nearly died while on a mountain climbing expedition, and he had to overcome hundreds of obstacles in his mission to keep his promise and build schools.
Potential exists in unlikely places - Time after time, children who had literally nothing proved to be apt students and only needed the opportunity to demonstrate their ability to learn.
Human nature is consistent - So many of the people Mortenson encountered are the same in every country and in every walk of life.
One person can be a powerful agent of change - An average American man made a positive international impact.
Respect for the traditions of other cultures - The title, especially, pays homage to this theme.
These sound rather trite, but they are the most obvious themes one will observe while reading this true story. Any truth which strikes a chord in you can be considered a theme, as well.