The shrewd Adam Swift makes a great point about boxing vs mma. Boxing promoters can afford to pay fighters more because they're not investing anything in the sport.
The UFC on the other hand is largely self sustained. It handles everything from television production, advertising, etc. in house. As a result it has a much higher overhead and is much more dependent on the live gate and pay-per-view revenue in order to have a successful show. In exchange for bearing greater risk, the company deserves a greater financial share.
Deciding which model is best for the fighter is not as a easy as saying which model pays better. In the short term, boxing's model may offer bigger paydays, but at the potential expense of the future. Promoters have little investment in future success, creating a make money now, worry later mentality that has hurt the sport.