A manuscript is an extension of you. In a way it's like a child---you create it, play with it, train it, and hope to share it with the world. But remember, you love your children like no one else in the world. You also love your manuscript more than anyone in the world.
You SHOULD love it, but. . .
It's easy to get too attached to your manuscript. After all, you've spent countless hours working to make it perfect. You've sacrificed time you could have spent with family and friends writing your masterpiece. You've weighed every word, deleted and reinserted the same scene several times, rewritten dialogue for weeks at a time. And now it's finished. And it's perfect. And YOU'RE NOT GOING TO CHANGE A DARN THING.
If you feel this way, you're too married to your manuscript. After you've spent months, or years, with the same story, it's impossible to see your own work. You need the advice of other writers, agents, editors. Change can be a good thing. Don't resist. Listen, weigh, and go back to your masterpiece. Usually you will see that at least a few of them are right.
When writers are too married to a manuscript, a red flag pops into the heads of publishing professionals. If you're unwilling to change a single word, a single scene break, they're going to think you're high maintenance. And you know what that means, right? In the words of my mother, "Don't throw the baby out with the bathwater." If a few changes could make the difference in whether you get published, consider making those changes. Consider listening.
Here's the disclaimer: If the suggested changes mean you have to compromise a theme or change the whole concept of the book, think long and hard before you decide.
On the other hand, if the changes are mostly window dressing, maybe you should make them. After all, it's better to improve your manuscript for your readers than to get your way.