Jeff, thanks for the link to the Masters Tournament Foundation 990s. As I read them, the MTF gets cash grants from Augusta National Inc. (the for-profit company which owns the club and runs the Masters Tournament) and uses them to finance, at least in part, the operation of Drive, Chip & Putt, the Asia-Paficic and Latin American amateurs, and donations to other non-profits. But ANI clearly owns and runs the Masters itself.
As to the broader question, harried course superintendents around the world aside, since the move to open membership to women, I think they're running their operation quite well. Augusta National enhances golf rather than detracts from it. Though I do wonder about the lack of birds in the air and squirrels on the ground.