One reason for this is that Brown Trout won't cross breed in the wild this way.
Nature sometimes knows best.
Rainbow Trout on the other hand can spawn either in the spring or fall.
Rainbows that spawn in hatcheries in the spring, will produce in the spring and Rainbows that spawn in the fall will produce in the fall.
This was explained to me by hatchery personnel, so balme them if I'm wrong!
Brown Trout can't be tricked into spawnning out of their natural cycle, so they are not used in hatcheries as much as Rainbows which can be. So there is a much larger window in which Rainbows will spawn, making them more productive for hatcheries.
Also as many of you already know, Brown Trout aren't as susceptable to whirling disease.