One of the hardest aspects of the publishing process for a writer is getting that first round of feedback from an editor. This is especially true the first time you have to go through it. Here you are, you've pored your heart into this story and pulled your hair out running it through over and over until you've decided it was absolutely and completely perfect. Now in steps an editor to tell you such and such a character doesn't work, this or that plot element is implausible, and by the way it all really falls flat in the end.
If you're not used to this, the natural reaction is to dig in and take the "you just didn't get it" stance as you resist any and all changes. Here's the thing about that - you're most likely wrong. Unless you're editor is completely incompetent (which you must assume they aren't since he or she bought your manuscript and must have known what they were doing at that moment), he or she is trained to spot these flaws and help you work them out. This is what they do and you need to trust them.
I can safely say that every change I've made to a book stemming from the comment of an editor has made the book better. Don't get me wrong, there are moments to refuse. Some things are going to be important to you and your vision. The process is a compromise and you're allowed your say, but make sure you have a reason for it. Remember that an editor in on your side.
I have to admit that I had a hard time early on in my career accepting this. I wasn't difficult or anything, but I always resisted in my own mind and it took a good deal of effort to realize that most of the time, I was wrong. Now I'm very open and welcome to the comments. I just had a wonderful conversation with my editor on my new novel and the comments I received were all insightful. Like anything, approaching this process with a positive attitude will always result in a better outcome.