Your seeing bad dmg on boss's because your playing surv witch has crap burst compared to many other specs.
But surv does very well on trash, probably better then most class/specs.
BM has amazing burst, but can be a bit complicating to open correctly.
If done well however, where talking about some of the best burst in the game currently.
It's a bit of a dilemma in that you have to choose whether you want high trash dmg and low boss dmg, or high boss dmg and low trash dmg, when choosing your heroic dungeon spec.
Alternatively you can change specs mid dungeon as you go.
Overall Hunter PvE dmg is pretty solid, and if what ive said in this post doesnt fit what your experiencing, then its very likely a L2P issue.