There was a time where most people didn't know how to operate a computer. We had to pull all the stops out to make computer use possible or easier for them - skeumorphism is one of the things that came out of that. We hoped that by emulating real-world objects, both in detail (see: iCal) or in more abstract terms (see: "3D" buttons).
Whether or not this ever really helped usability is a matter of debate.
In any case though, basically everyone knows how to use the computer and the web now. The general UI elements and their rules - links, buttons, sliders, etc, are all known to just about everyone. At this point since we've trained everyone, we get to drop some of the frills around the UI without suffering a substantial drop in usability.
That and it's just the style. Why are cars today more beveled and sharper-edged than cars of the 90s? Whatever happened to the big hair of the 80s?