One thing that many authors forget is that, for the publisher, publishing a book is a commercial marketing exercise. They may love what you have written and want to publish it – but it’s got to work for them economically, and often that means moulding it into a more marketable shape.
All publishers will want some input into shaping your book to make it more commercially successful (though publishing is always a risk and some projects fly whilst others do not). As an author, you need to be open to this, prepared to be flexible, and willing to make adjustments (assuming the publisher is not suggesting something so radical that it won’t look like your book any more!)
I once advised an author who had written a really good book and was looking to connect with a publisher. The publisher had a few common sense suggestions for tweaking the content so that the book would appeal to a wider audience and become a viable commercial proposition. In the end, the author wasn’t willing to compromise and would not budge on any suggested changes. Sadly, the book didn’t get published.
Having someone critique your work and suggest how it may be improved can cause understandable feelings of vulnerability. But in the end, being over-protective could mean that others don’t get to hear what you have to say.