I've seen a few women say that the rape scenes are very uncomfortable because of their own personal experiences, either being raped or molested and they don't want to ever watch it depicted on TV. I can totally understand that, I know guys who served in Iraq who can't watch realistic war movies/shows because it triggers intense bouts of depression and PTSD. As a guy who has never served in war or been raped there is very little on TV that will ever bother me, but I have enough empathy to understand thats not true of everyone.
Obviously we all know that rape really occurs in war and history and its a pretty brutal tool to dominate the enemy. Most of our books and TV shows are sanitized so that women rarely suffer and men act "proper". GoT is popular in part because it is a lot more realistic when it comes to war, power, nobility, honor, etc. But HBO/creators do have that popularity question, if they get too "real" it will definitely permanently turn off some parts of their audience. I don't really know if its better to have a gritty, realistic show that fewer people watch or a more neutered, tame show that more people watch.
To put it another way, I would stop watching the show if they showed penises and male butt fucking for 20 minutes every episode, as I'm sure many here would too. And we would complain about it to let them know why we have stopped. Well, thats what some women are doing.