This phrase can mean a few different things, depending on the context. Often it's used a little bit sarcastically, or when you're exaggerating, but you can also use it seriously. It's important to understand that saying "I wouldn't have it...." Means "I wouldn't choose for it to be...." So if you're using it, you mean that you want things to be that way. It definitely doesn't mean "I have no choice but to accept it."