It's a really difficult problem. So many of the things we do today are done on a rectangle with a screen. That doesn't make a good icon. Maybe icons are obsolete altogether?
And yet, people do grow up knowing that the green banana button means "phone" and the notched rectangle means "save", and often never even question "is there a real world analog for this icon?". It isn't that icons are obsolete: it is that we are graduating from a language of pictograms to a language of ideograms, yet for some reason we have large numbers of people telling us that that is somehow a horrible thing to do.
One explicit advantage that these sorts of icons have is that they allow for a nice symmetry between Save and Open icons and upload/download icons (Glyphicon is again a good example; see glyphicon-open and glyphicon-cloud-download). This ties into another, perhaps more arguable advantage, a blurring between local and remote save actions. As applications become increasingly web-based, device-independent, and portable, it makes more sense to me to intentionally separate the "save" action from it's destination; I don't care so much where or how my data is saved, I only care that it's save and that I can get it back later.
I'd love to hear responses to my thoughts here; they sort of developed as I wrote the comment, so they're rather fresh at the moment.