Most people think it's only about the money. Francis said it's the contract. It's the same reason why Fedor never signed. They own you.
It's phrased that you are an independent contractor (Like WWE does) but you are locked into an slave employee-like deal. They own your name, likeness, fights. Tell you where and when to be, what to wear, who to fight. Oh...and you get no health insurance.
An independent contractor is like a plumber that works for themselves. You call them, you negotiate a price and they'll work for you on a set day and time. They can also work for your neighbor or a company can pay them to do the work. That's how Francis thinks the contract should be or, the UFC needs to make everyone actual employees and provide the benefits that entails.