Jurassic planet

It's generally more difficult to domesticate a more intelligent animal as they have a greater capacity to disobey.

Indeed but like I said earlier, dinosaurs weren't very intelligent. A theropod would be hard to domesticate yes, but to train one might be easier provided it doesn't just see you as a snack.

It’s going to have to be some secondary factor that allows them to take over, then, like a plague or what have you.

Which as I have said before I will incorporate

Actually birds have a different brain structure from mammals that allows them to have greater intelligence while also being much more space and energy efficient, and given that birds evolved from dinosaurs it's entirely possible they were similar in that regard.

That's for the birdlike theropods though, the non-avian ones though like Hadrosaurs, ceratopsians, and the like weren't AS intelligent.

True, even without taking intelligence into account there is another factor that would make domestication difficult. Size, many dinosaurs were massive so keeping a number of them housed and fed might simply be impossible for a nonindustrial civilization.

"That kind of taming involves domestication or in the case of the less agressive ones just training them."

No, because taming or training on the one hand and "domestication" on the other are completely distinct things. Lions are easy to train, but nearly impossible to domesticate. Chickens, by contrast, are the other way around.

Not all dinosaurs were gigantic though, raptors were on average the size of turkeys.

Audiences generally expect a dinosaur-overrun After the End world to involve the biggest and most well-known ones. You could have packs of raptors hunting for prey, to be sure, but you'd better have some tyrannosaurs or there'll be hell to pay.

Nothing compared to what the reaction would be if you covered them in feathers.

My reaction to those people: "Fuck off, I'll make them look as realistic as I want."