Some babies are just noisy babies. My second little boy was that way. Does he cough? Is he horse (i don't know if that's the correct spelling for what I'm saying:).
It took me way too long to discover my second born (now 6 months) has GERD. It was atypical in that he didn't vomit, he swolled. He had a stuffed nose from birth, snored, progressively slept worse, lost his voice at like 1 month, etc etc. Your little guys is too little to just test medicines... I don't know what your doctor would recommend. Once my son got on the right medication (after a few tries) his stuffed nose, cough, etc etc were gone.
On the other hand, my first born had allergies to his environment. Our first apt, as it turns out, had mold. I didn't discover this until he was like 2. But I did buy him the top quality, no allergy, matress at about 2 months and a big part of the problem stopped.
Keep in mind that it's normal to check your baby's breathing. I think I got up every so often the first 6 months of my first born to make sure he was beathing. And, guess what, I'm doing it with my second. We worry, that's why we are parents. Keep an eye on him. Note the symptoms. Don't be afraid to call your doctor, or any other doctor for that matter, with questions. No one knows your kid better than you.
Oh, and the c-section. I'm in brazil, like a 80 to 90 % c-section rate down here. Crazy, I know. I doubt that's an issue. If anything, the fact that he was born early (depending how early) could mean that his sinus is undeveloped or something along those lines. At 3 weeks they are still figuring out the world outside. It's a bit bumpy at first. It'll all smooth out eventually. I know that seems like forever right now but it passes fast. Oh, and if you are breastfeeding, I have a norwegian friend who swears by dripping breastmilk in the nose in these kind of situations... never did it myself but doesn't hurt right. hehe