In Paul Johnson's tenure at Georgia Tech, Justin Thomas is the team's fourth prominent starting quarterback, joining Joshua Nesbitt, Tevin Washington, and Vad Lee. Being a run-heavy scheme that involves the quarterback as such, passing ability tends to be secondary in importance to things like rushing ability and capability at making reads on option plays. Those previous three quarterbacks were recruited with that in mind, and their stats reflect it -- between them, only Washington finished a season as the team's primary starter with 50% pass completion or better (56.4% as a senior in 2012).
Combine this with similar fortunes of several teams that have run similar systems over the last several years, and the narrative practically writes itself: Quarterbacks in this type of spread option system aren't very good passers.