This story is abusive.
This story is transphobic.
This story is racist.
These are all accusations I've seen leveled at writers. Each of them was brought up by one or two people from among hundreds of readers, and each of them was in no way supported by the text itself.
If you're a writer, you're going to encounter this one day. And you're going to take it seriously. Maybe you'll leap to apologize or reassure. Maybe you'll get paranoid about writing anything that pushes boundaries in the future. Maybe you will become cautious and try to over-explain things in author's notes or the text itself. Maybe you'll stop trusting your readers to be smart enough to understand what you're going for.
You will doubt yourself. You will doubt your ability to write in a way that can be understood, doubt your understanding of the world, doubt that you are a good person.
The "abusive" story had a moment of violence, and a reader projected her own history of abuse onto the narrative. She skimmed the apology scene and saw the fifth, sixth, twentieth time her abusive partner had begged for forgiveness, and she rejected the story as abusive.
The "transphobic" story had a character who had surgeries to make herself into what her father wanted. She suffered from learned self-hatred and the surgeries were a kind of self-harm. But a reader read the character as a negative metaphor for gender reassignment surgery, and so she called it transphobic.
The "racist" story had a racist character. It was a horror story, and one of the main characters was racist and sexist and horrible. The reader decided that a racist character meant the writer was racist and trashed her reputation online. The writer tried to defend herself, it blew up, and her reputation was tanked. I had a reader tell me she couldn't read my work anymore after I recommended one of this horror writer's stories. During the ensuing (private) conversation, I realized that the reader couldn't give me a reason why she hated this writer. She just did. So much so that my recommendation caused me to fall from grace in her eyes.
Readers will bring their biases to your work. Their histories, their traumas, their triggers, their hate and pain.
It is good and right to take their feelings seriously. But that does not make their interpretations correct.
It is natural to ask yourself if they have seen something you missed. If they have insight into your work that you don't. If they are right. If you have failed not just as a writer but as a person.
The truth, in all three examples I've given, is simply that the reader was triggered and also wrong. Yes, their feelings matter. Their feelings are valid. They should absolutely not continue to read your story, and you shouldn't try to make them. But their interpretation of the text is not informed by the words on the page. They aren't reading through logical eyes. They are viewing your work through their pain. Pain that wasn't caused by you but by someone terrible in the real world.
When you are accused, you needn't apologize or defend yourself or doubt everything you are. Simply say this: I'll think about that.
Because you will. How can you not? Who could avoid thinking about an accusation like that? Of writing an abusive, transphobic, or racist work? Very few writers automatically go, Psh, that's dumb. We are much more inclined to go, Are they right?
But when it's one or two people, when everyone else who reads your work does not have that same reaction... it is definitely the reader who is interpreting incorrectly. Feel free to scour the relevant scenes for anything confusing. Feel free to look for wording that might make someone misunderstand you. But I promise you, if you actually have confusing wording, more than one or two people will mention it. More than one or two people will get the wrong idea. When it is less than 5% of your readers assuming horrifying things, take heart. That means it's them, not you.
Be kind and keep trusting your readers. A few getting it wrong isn't the end of the world. Even if it sometimes feels like it.
