A 3-0 defeat in the capital, in which Emmanuel Agbadou was sent off in the first half, saw Wolves fall to eight defeats in 10 Premier League matches.
Supporters have turned on the players, head coach Vitor Pereira and the board and Johnstone spoke candidly after the latest loss.
He said: "It's just not good enough and we need to do better. We should be embarrassed.
"They might not want to hear it but we apologise to the fans.
"We're trying our best but we have to keep going. We've got good players and just need to turn it around quickly.
"It's difficult to find words. There's a lot of emotions. It's very difficult."
When asked what went wrong at Craven Cottage, Johnstone added: "Pretty much everything. We go down to 10 early, we concede early. It's difficult in the Premier League to have a man down and try to get a result. I think pretty much everything went wrong."