We don't know what was in Thomas' letter, but according to the video description it's
A lovely message from Peter Capaldi to my 9 year old autistic son. This arrived just before Thomas' nanny's funeral and helped him to deal with his grief in a profound way.
Jack Robinson is 4 years old, a huge Doctor Who fan, and has an inoperable brain tumor. No one knows how Matt Smith heard about the little Whovian, but according to Jack's dad, he loved the video. "His eyes just lit up and he was so delighted. It has made his day."