Is this normal for my new Cannondale Synapse Alloy 6?
No bike, no matter how good, is absolutely silent. It's possible that this bike needs to be tuned better, but more likely, it's simply the fact that it is Shimano's most basic 10 speed components and what is for Cannondale a more basic alloy frame.

I would suggest taking it to a different LBS for an opinion on what the real problem is, or if there is one.

It could be a loose or dry bottom bracket, headset, hubs, chain, chain ring bolts, saddle, seat post or pretty much any  other moving part on the bike. 

I hope that is helpful.