He was jeered with taunts of 'You don't know what you're doing' after substituting striker Stead, and later admitted it was a mistake.
"I've got to live with it, it's part and parcel of the game, and I certainly do know what I'm doing," Magilton said.
"I can't stop it and people pay good money to come and watch their football here.
"They're welcome to air their views and I know I can't go through my managerial life without getting any criticism.
"I'm a big enough person to deal with it. I never took the job expecting to be free of criticism."
Magilton added: "We've made a stuttering start at home and, after picking up so many points here last season, teams will come here and make it difficult for us.
"Palace did just that and probably deserved something from the game.
"After we scored it should have given us the confidence to go on and win the game.
"But it didn't transpire that way. We conceded another poor goal and that cost us three points."
Neil Warnock was delighted with his side's display and said: "It was as good as we've produced this season.
"We needed a performance like that and it took a good team to make us play. I thought our tactics were good.
"We looked strong, played some good counter-attacking football and overall it was a good match for TV.
"It would have been cruel to lose but had we scored a second it would have made it a bit nervy for them."
Warnock hailed new loan signing Craig Beattie and goal hero Moses.
He added: "Craig made a big difference and gave us something to hang onto. As for Victor, we know what he can do.
"I left him out a couple of weeks ago and told him why, but since then he's come back and played as though a weight has been lifted from his shoulders."
Next up Palace entertain Charlton on Tuesday evening.