Not sure about from there, but from our side, the timing through San Juan means a long boring 5-7 hr. layover as the flight to Bonaire doesn't leave till after 5PM. Wish I lived in NJ, I"d be on the red-eye,
Another good thing about the red-eye is you get there in time to eat breakfast, then go through the morning BMP orientation so you can be diving by 10 or 11am. Otherwise you'd have to wait for the 2pm(at Buddy's) or next morning most other places...
Personally I'm all for direct flights, playing around with the Divi or DAE weight restrictions and making another flight is just not something I'd want to do. Plane size flying over open ocean is a factor for me also.