I've travelled with my fly fishing gear a fair amount over the past few years and never, once had any problems carrying on boxes of flies. I've also had my lanyard and everything on it (nippers, forceps, etc.) in my carry-on luggage and never had any issues. I realize it only takes one grumpy person at security to cause problems. Just remember, no matter what the TSA we site says about carry-on items, the person agent at the security gate gets to decide what is carried on and what isn't.

For the record, the only item I was not allowed to carry on was a rod in a WOOD rod tube.