There's a great piece over at i09 by Catherynne M. Valente about authors and their response to fan fiction, in which she declines the urge to "holler about fan fiction being evil when I've made a name for myself at least in part by retelling fairy tales."
Anyone who knows and understands fairy tales will usually feel pretty comfortable with fan fiction. Fan fiction and fairy tale operate on a very similar basis. The best fairy tales don't simply retell earlier tales - they fill in gaps, twist the plots, upend characters, indulge in the odd bit of wish-fulfillment or revenge, and incorporate opportune bits from other tales.
Fan fiction is simply part of what makes the world of storytelling go around. It's not out of bounds to claim works like Geraldine Brooks' March are fan fiction. There are good and bad examples, after all. There is always a little trickiness around copyright - happily earlier fairy tale tellers didn't worry too much about that - and this has created angst and over-caution among some authors. It isn't that incredible in light of what can happen in the courts. Angst is probably also due to the reality that authors can access fan fiction thanks to the internet. Fan fiction was always being written, but the 'source' authors didn't generally see it until the proliferation of fan fiction sites. Curiously, television writers seem more apt at accepting and absorbing fan fiction, perhaps because much, even most, fan fiction is generated by serialised storytelling. Shows like Supernatural actively play to their fan base and you'll see the occasional wink to the fan fiction trends. Television shows also tend to have writing teams, with different writers working on the same stories, characters and arcs, pulling them this way and that as the series evolves. There is a different sense of proprietary rights involved, one a little more friendly to the generation of fan fiction. And most scriptwriters do spec scripts, which aren't a world away from fan fiction, either.
For myself, I think fan fiction is evidence of engaged, active, creative readers, readers who in turn become writers. I have nothing against having more writers in the world.