Redditor mister_ef comments:

The scene itself isn't the only thing that's screwed up, and actually wouldn't have been so bad if the set-up were there. I've been going over this scene with my girlfriend since we watched it. I've read the books, she hasn't. We've both read many of the major opinion pieces that came out in the aftermath of the episode. Based on comparing our two experiences, we've concluded that the show failed to establish a few key points that would have framed the scene in a more appropriate context:

First, watching the show it is easy to forget that Jaime and Cersei are not just sibling lovers, they are twin lovers. Think of all the stories of twins with strong connections bordering on the psychic. In Jaime's and Cersei's minds (at least before the events of the books and series), they are not just soul mates, they see themselves almost as two bodies sharing the same soul. They have given of themselves to each other wholly. Now, the concept of "marital rape" was largely unrecognized in our own society until fairly recently. In medieval times, it was just not considered a thing. Your spouse was expected to submit to you whenever you wanted, period. We know now, in our more enlightened time, that this is wrong (and I would never defend it), but in that culture it was not seen as such. Jaime and Cersei are not technically spouses, of course, but in their minds they share a bond superior to traditional marriage.

Second, the show really didn't do a good job depicting the developments Cersei's and Jaime's relationship. If you had only watch the show without having read the books, you might have gotten the impression prior to this most recent episode that distance had caused Cersei to fall out of love with Jaime (at least that was my girlfriend's takeaway). In that context, her protestations during the infamous scene are chilling. However, the books make it clear that she still loves Jaime, but has lost faith in his ability to protect and support her. Additionally, Cersei is extremely vain and feels that Jaime's loss of his sword hand makes him less of a man. Finally, Cersei has gotten into the habit of bartering sex for personal favors, and in doing so has commoditized her own sexuality. She dabbled lightly in this kind of commerce before Jaime left for war, but in his absence she became a pro. For all these reasons, Cersei has decided to leverage the withholding of sex (as well as any kind of emotional validation) from Jaime as a form of punishment, to go along with the verbal abuse she has also begun lavishing on him.

Third, the book does a better job of illustrating that Jaime has moved heaven and earth to return to his soul twin, and endured humiliation, maiming, and who-knows-what-else in the process, and upon coming home he finds she is playing childish games with him, denying him her affection and putting him down constantly. To Jaime, this slap in the face is a jarring wake up call, that perhaps he has matured in his time away from King's Landing and outgrown his twin. The horror of this realization is disorienting for Jaime. To put it in a more relatable context, it's like he just came home for winter break after his first semester at college to realize what many college freshmen realize; he's changed, but everyone else has stayed the same.

This context frames the scene in the sept somewhat differently. Cersei's protestations are petty, derived not from any real lack of consent but from a desire to be dominant. She's objecting not because of the sex, but because she wasn't the one that engaged it, and she hadn't finished punishing Jaime yet. Likewise, Jaime's forceful advances are not about sex at all, but more about a desire to re-engage Cersei in a more familiar venue, to see if perhaps the once-familiar rituals of coitus could ease his culture shock and repair their damaged relationship.

Unfortunately, none of this is readily apparent to a viewer who hasn't read the books. To make matters worse, it appears that this context was also lost, to some extent, on either the director, the show runner, the actors, or all of the above. It does not appear that anyone had this context in mind when they filmed that scene. For whatever reason, Lena Hedey and Nikolaj Coster-Waldau didn't film the deep, poignant reunion scene I described above, they filmed a by-the-numbers rape scene instead. Oops.

edit: tl;dr: The scene would be a bit less offensive in better context, but it still ends up being a rape scene when it's not supposed to be one. Personally, I'm going to pretend they recreated the scene from the book, and go on from there: Jaime isn't a rapist, Cersei isn't a victim, and that scene didn't happen.

For those questioning the rape scene, GRRM's response is to question it, too:

http://defamer.gawker.com/george-r-r-martin-distances-himself-from-game-of-thron-1565857941/+laceydonohue

10 gifs that offer evidence that this was not in Jaime's character: http://imgur.com/a/3hbS7

Example:

More on Game of Thrones season 4 episode 3, "Breaker of Chains" :

http://pandawhale.com/post/41753/reddit-follow-up-discussion-and-speculation-after-game-of-thrones-s4e3-breaker-of-chains

http://pandawhale.com/post/41655/game-of-thrones-season-4-episode-3-breaker-of-chains-gifs-and-memes