Gorilla Grodd was the primary antagonist of an entire arc, and he's primarily considered a Flash villain. Circe got one episode, Ares got an episode, Cheetah appeared here and there as a very minor threat. Black Manta existed to get shot in the face.
The Rogues aren't the only major villains that got very little airtime, but they had a really excellent episode.
And the Flash himself had great characterization throughout the series (enough to make him a fan favourite and Wally West perhaps the most recognized Flash), perhaps the greatest hero moment in the series, and his death in a parallel timeline formed the basis of the entire Cadmus and President Luthor arc.
Timm might think the Flash doesn't have a story that'd make a great movie, but I don't think he doesn't appreciate the character.
You're forgetting Giganta (Wonder Woman villain) who made a good couple appearances. And Orm (aka Ocean Master) who had two episodes.
Circe, as a singular character, got her own episode.
Ares, as a singular character, got his own episode. Plus a full movie.
The Rogues got clumped together and tossed aside.
Furthermore, to repeat myself, Captain Cold is treated like a total dunce in Young Justice. He's thrown away like trash at the
beginning of an episode. They made him a jobber.
Oh, and that bit about Wally West being recognized as Flash also upsets me since I'm a Barry Allen fan.