Despite that being a completely dad-rock list, I'd say most of it can be explained by how influential each song was, as well as how popular.
1) These are music industry insiders that made this list.
And that means they have good taste in music? No. Industry insiders are one of the reasons Top 40 is what most people listen.
Music insiders have exposure to more songs than the average person has. They also do research into what music sells and what doesn't. However, I will add the caveat that Frank Zappa told a guy who wanted to write pop music, that the kind of songs he writes will be dictated by the tastes of teenage girls.
The list was also created in part by people who play music professionally themselves.
All of the songs on that list are excellent, excellent tracks, but Rolling Stone's Top 500 list is one of the biggest jokes out there.
As I said, my own personal list would be different from theirs. However, who am I? I'm just a guy who studied music in college for a few years (decided to switch majors) and can sort of sing. I am not a professional musician that has access to the same variety of songs that Bono from U2 would have (for example).
As far as the complaint that top 40 is bad, this is not exactly new. People have been complaining about how bad "top 40" is at least since the 70s. So, we are talking about songs that were on the radio when people were complaining about how bad top 40 stuff is, yet still make a top 500 list decades later. Not exactly a small feat.
As far as recent stuff like Justin Bieber. Justin Bieber is better than much of the worst stuff from the 60s and 70s. The problem though is that there is nothing cutting edge in anything he does. Apparently, the people in the music industry who spend a lot of money to promote him (the SAME people that made that top 500 list) agree.
So other than your own personal opinion, why do you think that list is a joke?