There are many reasons. Most of those albums are widely considered among the best of all time because of innovativeness and influence on the genre, for example. And yes, Rolling Stone is a rock magazine (of course) so it stands to reason that their list of best albums will be a rock one.
And regarding Abbey Road: Well, as ludicrous as this may sound, I'm going to have to disagree with John Lennon on this one
The first half of that album is a brilliant showcase of songwriting, then it ends with I Want You (She's So Heavy), abruptly cutting off with no ending or fade-out at 7 minutes (or whenever it is) and going into Here Comes the Sun on the other half. That's probably my favorite moment on the album, the crazy awesome acid-rock cacophany of I Want You (the album's noisiest song, at that part anyway) followed by a bit of silence, then juxtaposed against the clean pure acoustic guitar of Here Comes the Sun. Every time I hear that transition, I smile involuntarily. Great stuff. Then essentially the whole second half of the album is incredible. That block of music is some of their finest work to me, from a total composition sense. There are hardly even divisions of songs, rather there are common themes and motifs that are woven throughout the record effortlessly. Track numbers are essentially meaningless after "You Never Give Me Your Money", and up until the very last song, "Her Majesty" (which is one of the funniest and greatest ways to end an album that I've ever heard). I know I'm not necessarily in the majority on this, but I feel that Abbey Road is sort of the culmination of all the skills the Beatles perfected over the course of their career. They effortlessly shift between different styles over the course of the album, their songwriting skills are at absolute excellence, their harmonies are gorgeous (the harmonies on "Because" are almost staggering, especially when you consider that John, George, and Paul sang them all in the same take without any clipping; they really ARE that in sync with each other), their instrumental work was excellent--essentially, it's just too awesome for me to write concisely about.
