The rebels also had fewer pilots and probably didn't have enough to field that many y-wings with dedicated gunners. He republic, however, had millions and millions of clones.
Did you see the celebration scene at the end of A New Hope? Where were all those extra pilots when the decision was made to stick an untrained farmboy behind the stick of a T-65? By my quick glance at the various camera angles I guess there are about 50 extra pilots in that scene.