It's Not You, It's the Audience

As I was scrolling through my twitter feed one day, I happened across the following:


Now, since this is an article is a reflective essay about the author's struggles with alcoholism, but that obviously didn't stop golden shower fans (links mildly NSFW) from latching on.
The takeaway lesson here is that you can't control how your audience reacts to your story. Although you can take steps to think about your story through outside eyes and head off gaps between authorial intent and what makes it onto the page, there are as many experiences of your story as their are readers.
Because we all we all interpret stories through the window of our own experience, it's not as though someone's take on your work isn't valid because it's not exactly what you intended. I've seen quite a few authors get fairly wound up about everything from unintended social critiques of their stories to weird fanfiction. However, there's not much you can do besides appreciate that people are enjoying your work, even if it's not quite in the way you intended (just accept that Rule 34 and Rule 36 happens).
Yes, it can be frustrating at times to have your intentions misread, particularly if you have strong views about the issues which arise in your story. But the only way you can write 'message' fiction that won't get misinterpreted is to bash your audience over the head with your preaching, which will chase away most of your readers (and it still may be seen as a parody criticising itself!). The most effective message fiction asks the reader to think for themselves by interpreting the story, and the inherent risk of asking people to think for themselves is that they may end up disagreeing with you.