I used to take all of my fly fishing things on board with me, but as previously stated it really depends on the local TSA to make the call. Since 9/11 I check everything, and always someone goes through the bag. It is easiest to have it in a good container right on top so they don't mess everything else up digging for it.
As also mentioned, it is sometimes easier to just send it in the mail.
I have found that by taking a few fly boxes, renting gear if possible, and buying local on trips makes everything easier.