The larger resorts wholesale a certain number of rooms to be booked by travel agents. In the case of larger resorts, a travel agent is the way to go. Smaller resorts can't afford to wholesale any rooms, so you might as well book with the hotel/resort directly.
In 16 trips to Negril, I have never booked a package deal. As you know flight prices vary day to day and I can get a better deal by being diligent and watching flight prices daily until I think they are at a low point, then book the airfare.
Hope this info helps.
Jah bless