The case I have is a Silverstone TJ10 and I'm still using the stock case fans. I have a 212+ CPU cooler for my i3-2120. I think the 212+ fan is quite noisy to my standards even at 1100 rpm I hear a noticeable hum. I have a few friends who own this same cooler but on cheaper mid towers and they swear it is completely silent. Is it possible that the case is amplifying the fan noise? I have well trained ears so I'm able to easily pick out sounds. I think my definition of silent is very different from his.
it is most likely air resonance in your case being amplified by the large, thin, side panels.
To fix it you need to put some thick foam on them. To test put your hand against the panel and push it in a little bit (not too hard obviously) if the noise stops then you have your problem otherwise it could be a bad fan (not just the CM 212 one) or you may just be more sensitive to it than your friends.