Cages are more economical, as you can track breeding dates, kindling dates, number of kits, feeding schedule, and environment of the rabbits. As @cassie said, rabbits are not very social animals(mine got in a fight last year, and almost killed each other). For rabbits to live together, they must be carefully introduced.
In colonies, the rabbits are VERY succetible to disease and predators, and you have no way of tracking what the rabbit eats, when it eats, when it breeds, where it kindles, and how many of the kits survived. Some argue that colony raising is the "fun" side of rabbit raising, and that could be true, if you carefully construct and organize the colony. But a poorly organized and constructed colony leads to TERRIBLE mishaps.