Still waiting for his first win since taking charge, he was left with regret but no excuses as League One side Rovers dominated their third round replay.
Rovers had the better of the open play and then sealed their fourth round place after winning the shootout by a 5-3 scoreline.
Fulham were never a threat in the spot-kicks after Jimmy Bullard had seen the first of them saved by Steve Phillips.
Bullard, who was playing his first full game since a knee ligament injury 16 months ago, had been his side's best hope with an outstanding return to the midfield.
Fulham packed a lot of power into their approach work and won the early midfield battle, but they were never allowed to make their Premiership status felt.
They had one really good chance early on when Clint Dempsey was through but a tackle by Steve Elliott near the penalty spot was deflected for Fulham's only corner.
It was Elliott's final contribution as he was stretchered off with a leg injury following the tackle.
Danny Coles dropped back from the midfield to take over and the changeover was seamless as Rovers continued to squeeze the Fulham attack.
By half-time though, Rovers were regretting their own missed chances.
A Dempsey challenge on home captain Stuart Campbell had the potential to see Rovers ahead.
The free-kick 25 yards out and almost in front of goal looked ideal for a shot by Chris Lines, but he decided to nudge the ball forward and no-one went for it.
Lines did his best to atone minutes later with a sharp cross after winning a long duel with Chris Baird down the right in what was a purple patch for the home side.
Fulham almost got back into the game early in the second half but Phillips dived to his left to fist away a volley from David Healy, before smothering a shot from Dempsey.
But Fulham faded late on and Rovers took advantage as the tie went into extra-time.