Have you ever disagreed with what your editor commented about your story? Do you follow all their comments?

Yes. But I do still accept *most* of the changes, especially anything factual or grammar-related, because I don't want my book to be *wrong.*
For comments based on story or things that are subjective, I then try to think like a publisher, and ask if the change will help the book meet its goals. I usually accept an editor comment if I know that I took the lazy or cowardly way out in the writing. I like it when someone points out that I could have pushed more.
When a story is personal to me and I don't care if anyone ever reads it or buys it, I do whatever I want, but I take on the risk of losing readers or buyers. (Young and Scambitious for example.)