Anne and Charles certainly do a lot for Scottish charities and organisations and Charles spends an awful lot of time up in Scotland. However, William spends very little time there, maybe a scattering of weekends at Birkhall for shooting during the year and a few days with Kate and the children in the late summer when the Queen and other members of the family are holidaying at Balmoral.
As far as I know William doesn't have huge specific interest in Scottish concerns and charities, and I think he has the Thistle because he is heir to the heir more than anything else.
By contrast, all the Queen's children have served as Lords High Commissioner to the Assembly of the Church of Scotland for a year, in Anne's case twice. IMHO I think Anne should definitely have received it. See Dman's post below!