And once again, if you are taking an inexperienced rogue in blues and PvP gear in a raid, then don't be surprised if expert Moonkin, Retadins, Fury warriors and Enhancement shammies (and all the other hybrids who will Suspect Something Is Up if I don't mention them) blast past him on the meters.
We're not sure if PvE rogue dps is too low. Some players clearly think it is. You can't just average out rogue dps across all WWS reports because you have no idea of the skill and gear involved without a lot of digging. Rogues are very sensitive to buffs and a lot of other factors. It's complicated and the solutions are tricky too. Just buffing rogue damage across the board could do bad things to PvP. Making them better now could make them way too good two tiers from now. These things take time sometimes.
We're also not going to keep anyone weak in PvE just because they are good in PvP or vice versa.