It is one of the earlier names of the brony fandom. The Herd is also a more all encompassing term for that fandom for those who do not wish to use the word brony or pegasis
person 1: I had the tv on in the background while playing CounterStrike and when i got up to pee I saw that a my little pony show was on.
person 2: my little pony?! lol lame
person 1: i don't know it was actually pretty cool:
random passer by: Welcome to The Herd
person 1: I finally watched that my little pony show you were talking about and i think i actually like it. I'm scared.
person 2: welcome to The Herd