Is it really okay to write a story with a bad ending? If not, why?

I am assuming my bad ending you mean the ending that does not work well with the story. I don't know why you would do that. If you understand the ending needs improvement, think about what should occur and improve it. If you think about bad as meaning the protagonist gets defeated, he encounters a problem from which he cannot recover or dies at the end, you have a tragedy. Many well-written stories have that kind of ending.