It's simple. The meta still favors high-DR characters, and even with the way Damage Penetration works, it's still not worthwhile to build because heroes can still easily reach 90% DR. Rogues, meanwhile, are some of the weakest heroes in the game. Being Fast is no longer special. You have Fast Casters, Fast Tanks, Fast Healers... All with better stats than the poor Rogues.
Solution: Give Rogues a new niche in the meta by giving them a class-specific buff! Casters have naturally boosted damage against Slows/Tanks, so why not make Rogues have natural Damage Penetration? Like 20%, or maybe half of the enemy's DR is ignored. Also, buff MK, BD, and Willow if you decide to do that. Because those heroes really need it.