I think, sometimes, people aren't aware that a slash indicates romantic or sexual pairings, and they just label the story X/Y because all of the other stories are labeled X/Y. There don't seem to be as many easy-to-find guides to fic headers and other fandom etiquette as there used to be, so a lot of newer fans end up guessing at protocol, and, when no one corrects their mistake, they continue to use it.

On the other hand, some people intentionally...over-label, I'll call it. I know I do from time to time, because I know some people in my fandom are bothered by the pairing I write. If there's anything in the story I think could be construed as 'shippy, I slap the pairing label on it. In the grand scheme of things, I'd rather disappoint the people looking for the pairing than squick or annoy the people who want to avoid it.

Edit: I see the conversation upthread, and I should say that the pairing I over-label for is het, not slash, so it's not a case of protecting the delicate sensibilities of straight people.