Occasionally when a story is "good but not quite what I'm looking for" an editor will say that they will accept the story providing I'm willing to make one or two changes.
This actually happened with my very first acceptance, a story called 'Standing Tall.' The story revolved around macho ideas of heroism, the way bravery in one situation doesn't automatically guarantee bravery in another situation, and the way that even when we achieve a victory we still have to taste all the other defeats life throws at us. The editor didn't like the downbeat ending as he felt the protagonist didn't learn anything from his experience. This pissed me off as not only was the protagonist obviously aware of the story's moral but ultimately it didn't matter if he learned anything or not, the important thing was whether the reader learned anything. The reader is a real live human being, the protagonist is just a fictional character, someone who only exists on the page. So the character doesn't have to understand anything so long as he communicates ideas to the reader.
Not only that but by making me change my story the editor was actually a living embodiment of the story's theme about the way life grinds you down by forcing you to compromise about things you care for. Irony can be a real pain sometimes.
Still, I was desperate to be published and the editor obviously wasn't going to publish the story unless I changed the ending. So I wrestled long and hard with my conscience for all of two seconds and then I sat down and started to make the changes.
Meanwhile another one of my stories got accepted by another editor without me having to make any changes. This story, Daddy's Little Girl, actually saw print before 'Standing Tall' and so is my first "real" acceptance.
Since then I've had other editors ask me to make changes. Some have been very helpful and I've been grateful for the editors' input. Others have been plain stupid.
On one occasion an editor said he would accept a story if I made changes but then neglected to tell me what it was he wanted changed. Another editor told me an acceptance was a dead cert provided I made changes to a key scene. I made the changes; he read it and promptly rejected the story.
A common occurrence is for an editor to ask for a minor change, "If you just change that one line ... " But when I see which line they want changed I realise its removal will render the rest of the nonsensical. "But that's the bit where the detective reveals who the murderer is!" The flip side of this is when an editor deems an entire story unworkable because of such-and-such a scene, completely ignoring the fact that on this occasion the problem really can be solved by just snipping a single line.
Even big name writers run into this problem. Alfred Bester used to complain how his editor made him add an extra couple of paragraphs to the end of his short stories in order to spell out exactly what happened at the climax. Left to his own devices Bester would have trusted the readers to be intelligent enough to figure this out for themselves.
Although, as I said earlier, sometimes the editor's input can be beneficial. In Danse Macabre Stephen King mentions how his editor asked him to cut a scene from Salem's Lot. King decided this was a good idea as the scene was too similar to one he had already used in one of his short stories.
Deciding whether to fight an editor over changes in a story is something that each individual writer has to decide for themselves. And the decision may well vary under different circumstances e.g. depending on how much you want the sale. I'm a lot less likely to argue over a story that's going to appear in high paying, high profile mass market anthology than a story that's going in a small press mag with a readership that doesn't even make it into double figures.
Another thing to remember is that even if you do make changes that you're not happy with there's always a chance of getting the story reprinted in its original format at a later date.
There's even the chance that by the time the story sees print you'll find yourself agreeing with your editor after all. In which case you'll have to apologise for shovelling all that horse manure through his letterbox.