Hughes coolly placed his spot-kick beyond keeper Simon Royce after Matt Fry had been penalised for handball.
Chris Lines fired Rovers in front from 10 yards after 16 minutes but Andy Barcham drew the Gills level, curling home a right-footed shot from 25 yards.
Stimson said: "That linesman gave more decisions than the referee on the day. Unfortunately when we had a great penalty shout in the first half it was on the other linesman's side. We got ourselves back into the game with a great goal and I was pretty confident at half time that we could go on to win.
"But we didn't pass the ball as well as we can with the wind in our favour and couldn't create many chances. Even so, I didn't think we deserved to lose. A draw would probably have been a fair result, but last weekend we won with a penalty and this weekend we lost to one."