Actually, they didn't. Rogues have been strong in every department throughout this expansion. The fact that they had abysmally low representation was, I'd say, in overall arena rep. If you looked at 2200+ ratings like we do now you'd notice rogue representation was actually fairly high.
The thing is, with things such as glyph of blind and sanguinary veins not allowing gouge to break on your bleeds, rogues have lost their retard checks. They have fallbacks. And then they have fallbacks for their fallbacks. This gutted the rogue skill floor to the extent that any joe schmoe can play a rogue at a moderately competitive level. The damage changes for PvE only exacerbated a problem that was already inherent in the spec.