Meulensteen's side went behind in the first half when Leon Osman opened the scoring for the hosts.
Fulham improved after the break and Dimitar Berbatov equalised from the penalty spot after the visitors had missed a couple of excellent chances.
Everton responded late on and fired in three late goals to make the scoreline appear more comfortable than it actually was.
Speaking to Sky Sports after the game, Meulensteen preferred to concentrate on the positives.
Meulensteen said: "The first half we just didn't get going but we had some words at half-time and I thought we were brilliant for 25 minutes after the break.
"We were positive, we pressed them. A couple of our lads had chances and we improved.
"I think Everton are bursting with confidence after recent results and they took their chances.
"We can do better and we will learn from this. We will certainly continue to work hard."
Fulham entertain Manchester City at Craven Cottage in their next fixture.