After only being on a new mountain bike for 6 months now I have to second what schwim said. Proper bike set up is worth working through yourself or having help doing and it will help your rear more than any padding will.
That being said I try to shop as smart as I possibly can and have been able to find two sets of the Fox Ranger Short with liner for mid $20 brand new. For what I spent on them they were worth the money. Mostly because of the liners breathability and their fit that help keep from chaffing on long (30+ mile) rides. Other than that it is just something everyone has to toughin up as they begin riding.
As a reference My rear quite hurting about 1 month after I started riding 3 times a week. Keep it up it will get better!