I'm not saying I approve but those are all much smaller ships. For Voyager in particular, they confirmed right off the bat that the ship was designed for atmospheric landing. I still think it stretches belief but not to the same extent as something as big as the JJprise - thisnk speed boat vs ocean liner. Same with the klingon bird of prey.
And the Enterprise is designed to be able to operate in an atmosphere.
This shouldn't stretch your belief any more than all the rest of the magic-wand-technology.
But it does, simply because it happens to be a fact in the films directed by Abrams.