"Thank you [agent/editor/publisher] for taking a chance on me/the book."
It's a sweet sentiment, born of gratitude. It's recognizing that there are thousands and thousands of people who are striving for the same goal that you've now achieved, people you feel no different from. Whether your little book is plucked out of slush or whatever happened, you feel special--the wallflower someone recognized was pretty and invited to dance.
It's a romantic view of publishing. And a fucking stupid one, so stop it.
Gratitude is a good thing (never, ever lose sight of it). Yes, be thankful for the excellent people you work with. Be thankful for their guidance and advice, the experience they share with you.
But any chance taken on your work is a calculated financial decision.
Publishers/agents/etc aren't doing you a "favour" when they sign your book or you as an author: they are making a business decision regarding something they think they can make money on. They are engaging in a partnership with another business--YOU. They are not the handsome prince saving you from a life of cleaning your evil stepmother's house in rags and singing to mice.
They took on your book, invested money in it, because they thought they could sell it to lots of people and make both of you money.
Yes, they love your book. Yes, they take on very few books. Yes, you've accomplished something great--you wrote well and you wrote something people might want to read. Yay you!
But this starry-eyed view of publishing/publishers/etc and advancement of the publishers-are-charity narrative doesn't help you. Instead, it makes it that much easier to be screwed over when you start viewing the weight of power as entirely on their side and none on yours.
You're a business. You're supplying something to a publisher--books--that they then supply to readers. Without your content, they can't make money. Sure, by "your", I mean writers in general--not YOU-you. There are always more books, more authors, etc. But you have far, far more value and power than you give yourself credit for.
I worked in acquisitions. And yes, out of 1200 submissions I'd only take a couple. A couple that I thought would sell. Books I loved that I thought other people would love too--enough people to justify the money spent publishing them. I wasn't doing writers any favours by accepting their work for publication. Doing favours would be a fast track to losing my job, which relied on picking profitable projects that I had to justify to my boss spending any money on. There's a gamble there, yes, as not every book will be profitable, even if it seems like a sure thing (and the more sure-things I did go with, the more room I had to gamble with other tougher sells). But I was making fairly educated guesses based on market trends, existing book sales, and my experience as an editor--I wasn't randomly plucking books out of a hat.
I was grateful to the writers who were submitting their work to me. Every time I got a fantastic, well-done book in slush, I thanked the publishing gods above and crossed my fingers they'd accept the contract and I'd have the opportunity to work with them. Hell, now I work almost exclusively with self-published authors now as a freelancer and I am STILL so damn grateful to get a well-done book to edit or have the opportunity to create a cover for a great novel.
You know who else took a chance on your book? You did.
You took a chance by writing it. You took a chance by submitting it for consideration and doing all the work that entailed. There are plenty more guaranteed profitable things you could be doing with your time. You have tons of ideas and characters speaking to you, you have to decide what to invest your time and energy in, and you took a chance on the one that you ended up writing. Do not give anyone more credit than you've given yourself when it comes to these "chances" that have been taken.
You have power as a writer. You have options. You don't have to accept a contract. You can request changes to the contract terms. Depending on the size of the publisher, you can speak up about cover art. You can question what your publisher is doing to market a book. You can remind them you are partners in this publishing endeavor who both want the book to succeed. Now, I suggest doing so with patience and friendliness, of course, remembering that people in publishing are hella-busy and spread thin. They're also people, not a giant faceless thing, but actual people who are worth being decent to.
But any publisher, particularly among small ones, who act like you should be grateful for the sheer fact that they offered to publish your book--who neglect to answer your business questions, or who respond to them with a "my way or the highway" attitude instead with reasoned explanations--is one to be cautious of. Yes, they provide a valuable service in publishing your book and getting it into the hands of readers...
So do you, however. You provide the book. You wrote something they thought they could sell.
And keeping that in the forefront of your mind--that you are a business, you have power, and publishing is about partnerships--is a less romantic view of things but ultimately a healthier one that will serve you better as your career develops.