This is an ever ongoing discussion in the field of interface design ever since floppy disks became obsolete.
Skeuomorphism is both receiving a lot of love and hate if you ask different designers. One of the problems is, that no one came up with a truly universal icon for saving and loading a file, so the ancient floppy disk has made it through the eras. Back in the day everyone was familiar with floppies and thus immediately could understand the icon. Today it is a relic that lost its roots in the physical world (ask a 12 year old what the symbol actually is), but maintained its meaning because of a learned pattern.
There are tons of articles, discussions, talks and what not regarding flat design vs. skeuomorph design and all their pros and cons.
One way of dealing with the lack of proper sign language for saving and loading that I can see in many programs is just getting rid of the icon and leaving only ctrl+s / cmd+s in place together with the save command in a drop down menu. My guess is, that a lot of developers would stop using the floppy icon if there was a well recognized substitute. Until then, the floppy will survive as a relic.