Don't confuse chakra manipulation with chakra control.

Chakra manipulation allows the user to control a huge mass of chakra to it's liking as to form a weapon ( rasengan or chidori )

Chakra control consists in flowing your chakra around your body as to perform jutsu, just how sasuke has to send it to his lungs and then turn it to fire and sakura to her hands and then quickly release it to make those super punches ( but she's a pro at it )

The rasengan does require some chakra control ( sending it to your hand ) but that comes easy to naruto since he has so much of it it's practically leaking out of his body.
The reason why naruto gets owned by genjutsu so much is because he's so bad at chakra control.