Actually, Nostalgia Critic hasn't really even watched it. He gave it a quick viewing then stopped, not because he hated it, but because he just didn't care. Whenever you saw him make a reference it was because he researched the show (which he admitted when someone asked him who his favorite pony was on "AskThatguy"). But he'll reference the show on his shows because he knows he has Brony fans and even claims they helped him out when he was trying to get back home from a convention.

TL;DR He's just a cool guy.