That's not true at all. Certainly not if you adjust for inflation as this list (made after Civil War but for the purposes of this discussion still valid) proves (
https://screenrant.com/highest-gross...ted-inflation/). Basically, all three Iron Man movies earned far less than
Spider-Man 3 did. The third movie, and the third movie alone, grossed a billion dollars worldwide but the real profits are in the domestic gross, and ultimately popularity is defined by the popularity with US audiences. IM-1 in 2007 made $312mn dollar domestic gross and compare that with Spider-Man 1's 2002 take of $403mn (which in today's money is $612mn), it's nearly $100mn less.
As for "none of the three actors are as beloved as RDJ" I don't know how we can measure that but RDJ by himself can't sell a movie (see Doolittle or the low-performing Sherlock Holmes movies). He's only successful as Iron Man. He ain't DiCaprio or Tom Hanks, both of whom can sell a movie by their mere presence. His solo movies weren't as successful as Tobey Maguire's Spider-Man movies. If you include the Avengers movies and also Captain America Civil War, maybe that goes up but I don't think one can credit RDJ entirely or majorly for the success of those movies. The Avengers 1 was sold on novelty, the first superhero team up movie, the promise of a Hulk who was fun to watch. Age of Ultron underperformed and was a relative failure. Captain America Civil War came off hot after Winter Soldier's word-of-mouth success, with the promise of featuring more team-ups, the hook of a superhero gang war, and of course Spider-Man.
Iron Man is also someone with a past as a war profiteer and arms dealer and most recently, around the time of Captain America Civil War, created a murder robot that destroyed an entire city and killed tons of people. Unless Peter has buried his head in the sand, it's hard to imagine him not knowing about this or not having some opinion about that. If MCU Peter had been configured closer to comics!Peter, Spider-Man would have sassed Iron Man about it. Instead the character has been conceived as a mascot and fan surrogate, and not an actual character with multiple dimensions living in that world. He's not allowed to have opinions.
As part of the reason for Tony being a more protected character than Bestman, there are obvious tells to allow his fans to see him off the hook even if the movie for its engine depends on us seeing and accepting Toomes' point-of-view and identifying with his vicarious revenge on Iron Man. But again the point is in the comics, that wasn't the case.
The Burglar didn't know who Peter was when he shot Uncle Ben either. He didn't know Ben either, heck he just met Ben the night he shot him. It's not like he killed a close friend of his or anything.
Because with Tony's great power there must come no responsibility and no accountability. Bestman, no name character, can be held accountable on the other hand. Which is why it's weak to shoehorn Tony Stark that way. It makes watchers of Spider-Man movies hate Stark but it also frustrates them because the movie still ends with the intent of seeing Stark as a good guy. So you get nothing. And it pits Spider-Man fans against Iron Man fans.