As Cynwise notes, the rogue population at endgame has been steadily decreasing pretty much since Vanilla. This is interesting because rogues haven't really changed as a class since Vanilla. There have been small changes here and there, but by and large the rogue class is still the same as it was at creation. Instead, the game has changed around it.
I've always thought the rogue was well-designed. In fact, if you look at the other classes, more of them have moved towards the rogue model than otherwise. So why then has the rogue population dropped?
I think that it's not one major reason, but several trends. The cumulative weight of all these trends has been to push the rogue population down.
1. Non-rogue melee dps specs became viable.
In Vanilla, pretty much the only melee dps at endgame were the rogues. Warriors tanked. Druids, Shamans, and Paladins healed. Sure, you may have had one or two offspecs running around, but the heart of your melee dps in Vanilla was your quintet of rogues.
Now, of course, all these melee classes can dps. Many of them dual-wield as well, occupying a lot of the rogue style in melee. As well, they also offer more options than the pure DPS class. They can tank or heal if necessary.
2. The new classes overlap with the rogue.
Both monks and death knights are melee dps. Indeed, both of them can dual-wield. Again, the overlap in kit causes the rogue class to bleed players to these new classes.
3. The other pure DPS classes lost a lot of their weaknesses.
Hunters lost their dead zone. Mages and warlocks improved their mobility, cut down on long casts, and gained more instants. Meanwhile, the rogue's fundamental weakness, melee range, has not changed.
4. Stealth has been marginalized.
The signature non-combat ability of rogues is stealth. However, because no other class (save feral druids) uses stealth regularly, it has become a mostly unused ability. The major use of stealth these days is to launch an opener, more than anything else. It is not really used in group play at all.
Think about this in terms of crowd control. In the past, rogue stealth/sap was the only crowd control which did not start combat. So sap had a lot of uses. Now though, all the ranged crowd control is easier to use and does not start combat, while having the advantage of not requiring the caster to get close to the mob.
This devaluation of stealth becomes really obvious if you play The Old Republic. TOR has 2 of 8 classes able to stealth, and that includes tanks and healing specs. Stealth is really powerful in group play, because many packs have one member that, if sapped, will allow the group to avoid the pack. This includes the non-stealthies in the group. Running an instance with a good stealther is a hilariously awesome exercise in avoiding as much combat as possible. In WoW, this type of gameplay is only possible if the entire group is composed of rogues and druids.
Stealth is also the only method to avoid running back from a wipe in TOR. The stealther can vanish if everyone is dead, and then res a healer who resses the group. Between these two elements, stealth remains relevant to group play in a way that it does not in WoW.
Those are the four reasons that I believe are causing the rogue population to decline in WoW. I don't think it's really possible to do anything about the first three reasons, mostly because it would make the other classes howl.
However, a concerted effort to make stealth more useful in group play might be possible. As well, I think the next new class should be a ranged stealth class. Making stealth more common gives a reason to make it more useful, while a ranged class would avoid cannibalizing rogues even further.