Cheika made the comment ahead of Saturday afternoon's Autumn International showdown between England and Australia at Twickenham, where the Wallabies have another chance to exact revenge following last year's series whitewash Down Under.
Aus boss Cheika believes that Will Genia and Bernard Foley in particular will be targeted by the Red Rose, but Jones says that his side will abide by the rules, as they seek a fifth successive victory in this heated fixture.
Asked about the 'bullying' claims, Jones told reporters: "I think it's a funny term to use. Australia vs. England games are a good physical contest. We've had four great referees in the previous games, and we're going to keep on playing hard but fair.
"There's a referee there to look at late tackles, and that hasn't been the case, so Michael's obviously looked at a different video to everybody else. I've coached over 100 Tests and every Test I've met the referee. That's a normal part of it.
"We want to show him respect because we want to tell him what we want to do in the game and he wants to tell us what he wants to do in the game. He's a bright guy. I don't think he's going to allow comments in the press to affect how he's going to referee. He's a professional, very good, young referee. I'm sure he's going to do a great job."
Australia's last win over England came at Twickenham in the 2015 World Cup, coming out on top 33-13 in the Pool A clash.