Ashkan Dejagah's 57th-minute opener at Craven Cottage had looked set to secure Meulensteen three points in his first game in charge.
However, long-range efforts from Vlad Chiriches and Lewis Holtby extended the hosts' winless run in the top flight to six matches, although Meulensteen is keen for his players to take positives from the performance.
"It is very, very hard to take. I thought we were good, well organised," he said.
"I said to the players before the game I want an inspired performance and from a tactical point of view a disciplined performance.
"We got that and it got us to a point where we were on top and winning 1-0. That first goal of Tottenham's came out of the sky. (It was a) good strike but it smelled a little bit of offside, looking back to (Jermain) Defoe's position.
"The players responded well after that and (even after) a great strike from Holtby we kept on going and threatening the goal.
"A defeat is very hard to take."
Fulham host Aston Villa on Sunday as they look to record a fourth top-flight win of the season and climb out of the relegation zone.
Meulensteen believes his side have shown glimpses of what they are capable of ahead of Villa's visit.
"Every club and every manager is different but we can all agree that every positive result or performance always starts with hard work, commitment and discipline," he added.
"That's what we got tonight. That is how we win the fans back and we did that."
