Prothero was the head coach of the Willamette men's golf team for 44 years from 1966 through 2009, and was the head coach of the Bearcat women's golf team for seven years from the team's first year in 1995-96 through the 2002 spring season. Prothero impacted many Willamette students in positive ways, not only as a golf coach, but also throughout his 46 years as a member of the faculty in the Department of Mathematics.

He recorded the second longest tenure for a Northwest Conference head coach in one sport. He trailed only WU's Lestle Sparks, who coached the Bearcats in men's tennis for 50 years (1925-74).

Prothero led the Bearcats to six NWC championships in men's golf. He also guided the team to eight NAIA District 2 titles, with the team advancing to the NAIA National Championship tournament in each of those seasons. In 1975 and 1976 the Bearcats finished 14th in the nation. He coached six men’s golfers to a total of eight NWC individual titles

Under Prothero’s guidance, the women’s team won conference titles in 1995, 1996 and 1999. The Bearcat women advanced to the NCAA Division III National Championship tournament in 1998 and 1999. WU also claimed the NWC women's individual title in 1999.