So you bore witness to a teenage girl in the aftermath of a sexual assault... and you went on to write a story about a girl being raped. This post has been enlightening, though I'm not sure what point the rambling final paragraph is supposed to be making.

"scientifically it's not rape if she likes it. "
Cite your sources. Culturally, socially and legally, it's rape if it's anything other than both parties consenting freely and without duress.

"Do stories like these effect people who actually get raped?"
YES. One in four women are survivors of sexual assault, and even mentioning the topic can cause them to recall their incredibly traumatic ordeal.

"Are you doing anything to stop it?"
By protesting and discouraging stories like this, it sends a message to people that rape is not acceptable in any circumstances and totally unjustifiable. You probably didn't intend it, but by having FS 'like' it in the end encourages this bullshit male attitude that "oh, women just don't know they want it". It's what rapists use to justify things in their head.

611768
Pacings of the internet in a nutshell

612533 lol

I wrote a story about a shy pony getting "raped", but scientifically it's not rape if she likes it.

BS. The difference between rape and consensual sex is not scientific, so trying to make any scientific distinction is impossible. I've heard a similar argument about how "it's not rape if she orgasms." The person who said this was convicted of rape, and rightfully so: an orgasm is a mechanical response, not a "yes".

The only real way to distinguish between rape and consensual sex is the presence or absence of consent, hence the term "consensual sex". Clearly, Fluttershy didn't consent, even if she did enjoy it a tiny bit. In all honesty, the fact that you don't seem to consider what happened to be rape worries me. The "she enjoyed it" argument is often impossible for prosecutors to disprove, thus making it an attractive excuse for rapists who don't want to to get busted. That's why, in the real world, the only thing that matters is whether the alleged victim consented.

If I were living in Ponyville, and I somehow knew about the rape, I would encourage Fluttershy to tell law enforcers about what happened. Hopefully, they would be able to put Iron Will behind bars, before he does the same to somepony else.

As for rape in the real world, you're right: people like me aren't doing a whole lot to help. But, that has nothing to do with your fiction. Even if everyone was doing something to stop rape from happening, that doesn't make this story any better, IMHO.

PS: "no" does not mean "yes", and "yes" does not necessarily mean "anal" (especially when the word "no" is used instead of "yes").

BTW, in your description, you make it sound like the sex was Fluttershy's idea. But, in the story, it clearly wasn't. Moral arguments aside, this should probably get looked at, if only to make the story and description consistent. I would strongly recommend changing the description to better match the story, since the description is easier to rewrite than the entire story.

Also, putting a warning about the story containing non-consensual sex might be a good idea.