I believe it was just some dumb joke they made in the first episode about El Chapo. Not expecting the pod to go anywhere, they chose to name it that. Then it just stuck.

Chapo Trap House is a popular left-wing podcast. That’s how the sub originated, but it quickly grew into its own separate thing from the show, being a catch-all left-wing shitposting sub. Really great community with lots of great in-jokes. Hoping this takes off here. CTH was the only sub I really browsed on Reddit.