Several reasons.
1. The amount of money wagered in trifecta pools dwarfs the the amounts wagered in the other pools.
2. The larger number of combinations allows for larger variances from "true" odds and what I think is a big factor
3. There is no board that tells you what the odds are for each trifecta combination. If the knowledgeable public "knew" that post #1 had about a 20% chance to win the next game and they looked up at the tote and saw odds of 10-1, I guarantee you that post #1 would not go off at 10-1. This cannot be done with trifectas.
4. The public also has a tendency to box their favorite or better players. This doesn't work very well in Jai Alai because (assuming each player has equal ability) each combination is not equally likely to come in because of the mathematical set-up of the game. This becomes painfully obvious when a "hard" combination comes in and it pays less than half of what it should pay. This overplaying of "bad" combinations along with the avoidance of some "good" combinations creates the profits (and doubly so in the twin-tri).
Joe.
Joe.