I think there are several reasons why it isn't held in the same regard as November Rain by the general public (I think that the fans tend to agree it is an amazing song). The first is the length, as previously stated. Secondly, maybe the public was a little tired of epic ballads when it was released, since it came after Don't Cry and November Rain, and this meant it slipped under the radar a little. Lastly, I think a lot of it has to do with Kurt Cobain and his grunge buddies. They changed the musical landscape to one that embraced simplistic music, with low-concept videos, making a statement that they as artists were in it purely for the music. To many, Estranged simply highlighted just how out of sync with the general music industry Guns N Roses were at the time. This was the moment where many critics claimed that Guns had jumped the shark (http://en.wikipedia.org/wiki/Jumped_the_shark
) and weren't a viable creative force of the time.
I think this is why the fans love the song, and those who tell us what to like generally ignored the song at the time, or mocked it, as it was the safe and "trendy" thing to do.