Does this sound familiar, either to writers or editors?
A young writer recently complained that when he handed in copy, the material returned to him resembled nothing like what he turned in.
His complaint was that the finished stories did indeed read tighter and flowed easier -- but that he was missing a chance to help with the changes, and not getting any feedback.
Here's what I'd say:
If your copy is being rearranged big time, a couple things: First, count yourself blessed to still be writing for them. If you still are, that means you've at least got the basic research in and they're willing to rework -- and you still have the income source. Sometimes if there's a lot that needs done, they'll write the writer off. I had a publisher who insisted on it.
Second, look at what they did, sentence by sentence. Next time you think you're done, put it to that test they used, and do those things to it. The other thing the editor could have done is said to you (irritated or not): "This is completely inside out and unacceptable. It needs this, this, and this. Fix it." For some mags, that's their policy.
Either they didn't have time for that, or it's not their policy, or they didn't think you could do it on your own, or they don't know you well enough to know you could on their short deadline, or they have someone who is free to fix things up and they're okay with it. They may know there's a learning curve to writing their style and they're willing to cut you some slack.
One thing you might do is ask, politely, proactively, positively: "I noticed there were some changes made to my story. Can we go over them so I'll have a better idea for my next piece of what you're looking for?" (which beats "How dare you change my story!" cold ...)