After earning his master's degree from Illinois State in 2004, Dougherty embarked on a five-year tenure at the University of San Diego.
One of the receivers Dougherty coached was All-American, team MVP, and later Philadelphia Eagles signee Michael Gasperson.
He mentored Josh Johnson, who became USD's all-time leading passer and was selected by the Tampa Bay Buccaneers in the 2008 NFL draft.
Johnson has spent 14 seasons as a professional football player, currently as a backup quarterback to Lamar Jackson with the Baltimore Ravens.
Dougherty tutored four of the ten all-time receiving leaders in school history: Jaydon Mickens, Jermaine Kearse, Kasen Williams, and Devin Aguilar.
Quarterback David Fales, who went on to be selected by the Chicago Bears in the 2014 NFL draft, passed for over 4,000 yards that season.
Dougherty added the title of assistant head coach in the 2014 season, during which he mentored quarterback Joe Gray, who tied a Mountain West Conference record for consecutive 300-yard passing outings.
In 2018, the Bruins' leading wide receiver, Theo Howard, made 51 catches for 677 yards and did not drop a single pass all season.