What is wrong with Joe's and Janie's relationship?
That's a really good question. To sum it up, I think the problems in the relationship between Janie and Joe lie in the lack of equality and mutual respect, which are pretty much the foundations of any solid, healthy, and enduring relationship. Equality doesn't always have to mean that the persons have to vote as equals on every issue, but it does mean that each person is valued and has a say in the decision making processes.
If you are writing an essay or preparing a report on this topic, you'll probably want to bring up and discuss concrete examples from the novel, beginning in chapter 6. You'll find specific instances, for example, in which Joe wants Janie to dress up (for show, to impress others), to keep quiet (he gives speeches but doesn't allow the same for her), and to cover up (Janie's hair is a central concern of the novel, in a serious -- not trivial -- way).
I just finishing reading and discussing Zora Neale Hurston's novel Their Eyes Were Watching God with my college students in a Literature of the South class. I'm glad to see that you're reading it, too.