There's an interesting article in the October issue of Smithsonian magazine about how our brains process music (How Music Works by David Byrne of The Talking Heads; and if you don't subscribe you can read it here); apparently excerpted from his book by the same title. In it he talks a lot about how we experience music, and how that's changing now that the world is basically immersed in music.
In the article Byrne also cites some studies by UCLA neurologists who monitored human brain activity as they were exposed to actions and emotions of other people. By determining which of the observers' neurons fired, they decided that we physically and mentally "mirror" what we see. Basically what that means is when you watch someone running track or having a temper tantrum, the neurons associated with the muscles used for running and the emotions deployed for a snitfit light up in you. They concluded that while we can't physically benefit from the neurons firing (to get the benefits of running track, you actually have to run the track) we're all hard-wired to be empathic.
As with music establishing empathy with ficition is not a face-to-face process; readers depend on writers to provide a story that engages and entertains them while writers are dependent on the readers' interest and imagination. Musicians use instruments, lyrics and their voices to do this while writers are dependent solely on words, but they work the same way. When you hear an engaging song it produces an emotional response: happiness, sadness, nostalgia, regret (which is why Adele had so many sniffling through the morning commute; the songs she wrote after having her heart broken seem to resonate with anyone who has ever been burned by love.) Writers go after the emotional connection primarily through characters and conflict but also by creating an artificial reality for the reader to explore. The strength and endurance of that emotional response is the empathy yardstick.
I've heard it said that there is nothing more artificial than art, and in some cases that may be true, but I think it depends on the artist and maybe what neurons are firing in their brain during the act of creation. I know how I feel when I write in the zone, which is always my goal; I've often described it as sneaking out of the house at 2 a.m. on a school night + going on a wild midnight joyride + waking up Christmas morning. A quote I read in a Times article on Sunday summed up some of that in six neat words: "Get on my train. We're leaving."
When you're working on a story, you are both the author and the beta reader. You may not be conscious of the emotion you're pouring into the story, but it's there, and at some point you should consider how the reader will probably react to it. You may be able to do this while you're actually writing; I use my daily editing session to think about how what I've written will impact the reader. Having several hours break between the writing and the editing allows me to put a little emotional distance between me the writer and the story to allow me the editor to analyze it. One of the most common ways to spot readers empathy problems is when we find ourselves skimming our own stories; if we're not interested in reading it then there's a good chance the reader will have the same reaction.
Once I've finished a book, I do a comprehensive technical edit, revise, and then a second complete read-through to make my final changes. It's during that last, start-to-finish read that I again consider the reader's response to the story. Is it exciting to read? If I'm skimming any part, that's not. Did I deliver interesting characters? Are these the kind of people a reader will care about and root for? Is the pacing consistent and absorbing? Nothing kills the momentum of a story than passages that slog along. Are there plenty of good reasons to keep turning the pages? That's really the final question -- will it be read by someone I can keep engaged from start to finish, and afterward will they feel it was time well spent? If I've served the story by genuinely investing it with my energy, my emotions and my sense of wonder, then there's a good chance that the readers will mirror me.