Adam Johnson stole the show at Craven Cottage, grabbing his first Premier League hat-trick and setting up Ki Sung-Yueng for Sunderland's other goal.
Steve Sidwell was on target for the hosts, but his goal failed to prevent another resounding loss for a side beaten 6-0 at Hull City last month.
Meulensteen remains adamant Fulham, who are now just one point above the relegation zone, are a better team since he took over from Martin Jol on December 1.
However, although the club have picked up three league wins under Meulensteen, they have now conceded 46 goals - comfortably the highest tally in the division.
"In general, the transitions, performances and the way we want to play have been improving, you can’t deny that," said Meulensteen.
"If you look at the stats, in terms of possession, attempts and all sorts, we are better.
"But within those regards, the quality in the final third, the final ball and putting the ball in the net, that’s one issue.
"What we keep talking about that we need to get out of our system is conceding those goals."
Meulensteen admitted he felt “disillusioned” after Fulham's first defeat of 2014 and felt goalkeeper David Stockdale should have done better with Johnson’s opening goal.
He added: "It was one of those games which we controlled and dominated and should have been two up before they put that free-kick away.
"I think it was saveable. He [Stockdale] got his hands to it, but just not enough power on it to knock it over the bar rather than in.
"You give yourself a mountain to climb. You make it really hard work to get back in to the game and get something out of it knowing that these home games against teams around you need to be won.
"You end up sat here, 4-1, no points and feeling very disillusioned to be honest."
