Now, I'm not saying you can't have opinions. I'm not saying you have to agree with your editor/agent/designer/marketer all of the time. I'm also not saying you are forbidden from voicing your opinions. All I'm saying is you really, really don't want to be labeled as "difficult to work with."
The fact is, if you are looking to be traditionally published either by the "big six" or a small press, you have to relinquish a substantial amount of control over your creative work. When you sell a novel (heck, even from when you sign with an agent), from there on out your book becomes a collaboration. And collaborating doesn't mean you get your way all the time. It means you work together, that sometimes you have to put aside your "vision" and accept that maybe your agent/editor/designer/marketer knows better. It requires trusting that you're in good hands.
If you want to do it all yourself—and that is totally fine and cool if you do—then I would look into self-publishing. That's the awesome thing about that route: you do have complete control over every step. Some people do really great with that (I am definitely not one of them, but admire those who have that skill set.).
For the most part, I think writers know this, but then I hear stories about "difficult authors" from publishers and how hard it is to deal with them. With smaller publishers, I have actually heard that it makes a big impact on whether or not they buy another book from that author. They have smaller lists and work very close with their authors (some small presses only have a handful of employees, after all), and if that author is always hard to deal with...yeah, sometimes it makes more sense for the small publisher to move on.
Again, that doesn't mean you have to be happy with everything your publisher does, but when you do have worries be professional. State your concerns without being accusatory. Be polite. Ask questions before you jump to conclusions. And remember that those you work with are on your side. They believe in your story and are doing their best to make it into an amazing book. Gratitude always goes a long way.