rock the boat is to risk upsetting a group situation. Example: "We have to work together on this project. I don't want anyone rocking the boat."
People in a group on a small boat need to work together. If one person moves suddenly, the whole boat could rock dangerously. Example: "Everyone wants to go except for you. Why do you have to rock the boat?"
We cause trouble for other people when we rock the boat, because people need to find new positions to make "the boat" steady again. Example: "I hate to rock the boat, but I do think we need to rewrite this report."