Broad brushed off a hostile reception from home fans at the Gabba to take five for 65 and restrict Australia to 273 for eight at stumps.
After his controversial role in last summer's Ashes series, Broad was the subject of much heckling before and during play.
The Brisbane Courier-Mail has even refused to print his name but Atherton felt he thrived in the situation.
Atherton told Sky Sports: "The cricket correspondent is going to have quite a difficult job writing a match report tomorrow without mentioning his name.
"He is the kind of guy that will react well to all that kind of stuff.
"He is not easily intimidated, he is not easily ignored and he had a great day."
Andrew Strauss, who captained England to their series victory Down Under three years ago, thought Broad's performance changed the course of the innings.
Strauss said: "After the first hour I think England were worried.
"They were thinking they were not sure they were going to get many wickets on this.
"Stuart Broad really went hard at Michael Clarke and from that moment on Australia have been on the back foot.
"It was a very professional day's cricket from England and Australia will be bitterly disappointed."
Broad claimed the key wicket of Clarke shortly after lunch when he forced the Australia captain to glove a catch off a short-pitched delivery to short leg.
Broad also troubled Clarke in the summer and Atherton believes that is an area of concern for the hosts.
He said: "I think he struggles against the taller bowler.
"Because of his bad back and various things he doesn't like to duck or finds it difficult to duck, so he likes to stand and play the short ball.
"So if you have got a tall bowler who can get steep bounce from not that short of a length it gets him into difficulties.
"It really couldn't have gone any worse for Michael Clarke, from a team perspective - this is a below-par score on about as flat a pitch as you can get - and for him personally."
Another former England skipper, Nasser Hussain, was surprised a number of the Australian batsmen had difficulties coping with short-pitched balls.
He said: "It was a bit of role reversal. We used to come here in the old days - or any side from around the world - and get surprised by the bounce at the Gabba, and play shots outside off-stump, nick off and get caught behind.
"It was Australia doing that on this occasion, on their fortress, a ground they don't lose on and don't get bowled out cheaply.
"It was a very un-Australian-like performance. There were quite a few soft dismissals at the top."
Former Australia spinner Shane Warne shared the concerns about Clarke and the rest of the top order.
He said: "All in all it is the way they got out that has been the most disappointing factor.
"I think it has just been a bit soft, a bit timid. There hasn't been enough aggression.
"I think also for Michael Clarke, I think it is the type of bowler.
"I think what he has got is a little bit of a problem with that angle, but also at times he has had his back issue.
"I think that has got him out and stopped him being aggressive. Instead of seeing it and trying to play that short ball he is just trying to get out of the way.
"I would like to see him go back and playing it, taking it on."
Another revered former Australian star, Mark Waugh, was in agreement.
Waugh told BBC Radio Five Live: "The batting is a bit of a worry for Australia.
"There was some pretty loose strokeplay from a lot of that top order.
"They batted like they have never batted at the Gabba before. They hung their bats out and fished at wide balls they could have let go. Some of the dismissals were very ordinary."
Australia did show some defiance as Brad Haddin (78 not out) and Mitchell Johnson (64) put on 114 for the seventh wicket.
In an interview after the close of play, Johnson said Australia were "definitely back in the game".
But Strauss said: "He's trying to put a positive spin on it. He knows in the dressing room they have fluffed their lines to a certain extent. Up here you need 400 on the board."