I posted this in a different forum but i'm going to post it again. To help everyone understand why they do so much damage. This is a copy paste from a post i read on WoW forums. I found it very informative.
A normal pet melee attack/Claw does about 6800-7000 damage depending on gear.
This is without any benefit from the Cd's/trinket/passives.
Now lets start adding the raw % bonus it gains from different spells/abilities.
+ 20% from Bestial Wrath
+ 30-35% from PVP power
+ 12.5% additional PVP power from Rapid fire and 4set bonus
+25% from Stampede.
+ 10% from 3000 mastery (Spirit beasts blessing)
+ 100% to the first three Claw/Bite/Smacks from the passive bonus.
So we're up to ~100-110% of the normal Melee damage , and 200-210% the normal Claw/Bite/Smack damage,lets move on to RAP/AP scaling.
100 Agility translates into about a 50 damage increase to pet melee attacks.
Normally you'll have a use trinket which gives you around 4000 extra agility on use.
So your pets Melee and Claw damage is increased by about 2000 damage.
Then we have Rabid which gives your pet 25% more AP and about another 4000 bonus to it's melee damage hits (It scales from it's current AP so that extra AP from agility,yeah..)
So with all your agility and AP benefits you're adding about 6000 damage to melee and claw.
Then add 100-110% to Melee and 200-210% to claw from abilities and spells.
So what does this mean? Well.... your "main" pet does-->
Max Melee hit: 18.000-20.000
Max Melee crit: 34.000-40.000
Max Claw hit: 38.000-40.000
Max Claw crit: 76.000-80.000
And your Stampede pets does about half of that damage as they don't seem to gain from anything else than the 25% Stampede buff, mastery and PVP power