You must own a convertible. LOL Just kidding.
Yes, it will make noises. There are some things you can do to help lessen squeaks in the joints (grease them) and rattles where the top meets the header (there's a felt strip in there that wears out), but it will never be completely quiet.
If you want to feel better about it, hop in a Jeep Wrangler. That's what we used to have and the Boxster is silent in comparison.
If you want to feel really good about having an expensive car that makes a little noise, hop in a convertible Corvette. Besides having to manually put the top up/down in a $50K car, it's still a Chevy and it makes all kinds of noise.