Goals from Heidar Helguson, Akos Buzsaky, and Tommy Smith sealed the game for Q.P.R. despite Hugo Rodallega's consolation for the Latics.
Speaking about the game, Hughes said: "Well it's just the start and I have explained to them they have to maintain what we produced today and keep working hard in training.
"The work ethic and the desire to do the right thing and stay in the Premier League is there for everybody to see and I am delighted for the players.
"We kept [the win in midweek] in our thinking and the win on Tuesday helped today. It is a good habit to have back-to-back wins and we will look ahead to the cup game next week and enjoy it.
"We will take every game as it comes and I was pleased with what we produced today. The guys were excellent all over the pitch and it is a great reward the three points."
Hughes has replaced Neil Warnock as manager at Loftus Road following the former Sheffield United manager's sacking in early January.