The other day, I did a heroic Lost City of Tol'vir run with my guild.
As Marks spec, I naturally fell to second place on the DPS meter, about 2-4k DPS short of our Surv spec hunter in the first couple of boss fights.
However, I had to laugh when we jumped up onto the croc statue heads to do Lockmaw, because whilst I set my pet to stay on the ground, the Surv hunter didn't - meaning his pet was out of action for the whole fight.
Guess who was top DPS then? Yep, me.
One of the main reasons I've been proud of my "BM spec since beta" tag is because back when I first joined my guild and started raiding Molten Core, none of the hunters cared about their pets. MM was pretty much the only decent DPS spec back then and pets were fairly weak. Even so, I as a BM hunter consistently held my own in comparison to the other hunters merely because I used my pet as much as possible... and managed to convince a few to at least rez their pet occasionally, if not use it.
So, if you're a hunter (or any other pet class, for that matter!) and still don't know how to handle your pet, go learn how (yes, I really should update those pet control posts for Cataclysm... will try and do that at some point), because they do great DPS even if you're not BM! :)