Wenger withdrew striker Olivier Giroud for midfielder Francis Coquelin during Saturday's goalless draw at Aston Villa, sparking chants of 'You don't know what you're doing' from the visiting fans.
Arteta respects the right of supporters to voice their frustrations but insists Wenger has his reasons for every decision he makes.
"They can say whatever they want," Arteta told Sky Sports News.
"If they feel that way it has to be respected. Even when they say something to one of us.
"I think he has got experience and he has been here for 15 years. He is someone who knows the club better than anyone.
"He knows the players really well and he knows what he can get from each of us.
"So when he puts the team out, obviously it's because he wants to win it and he's picked the best team - that day - to win that game.
"He is always trying to do the best, you know. And some of the decisions he takes are very unpopular. But if he takes them it's because he's got a reason.
"If he does it once then maybe it's a mistake but if he does it four or five times then there is a reason why and he'll explain that better than anyone."
However, the focus of the French coach remains unmoved.
"My job is to give full commitment to this club, with integrity. That's what I always do without expecting any return," Wenger said.
"I don't want to comment on that [fans]. I just make sure that I do my job properly - that's what I do."