I've flown to NY twice on Delta post 9/11, and both times I've just carried it on and was never even asked about it, and both times it was a pain in the ass. Even if you got your board strapped on your backpack backwards so the graphics' against the backpack and the wheels/trucks are part of the bag mass, it makes your backpack 2 inches too thick to stow away in the overhead compartment, both times I ended up just flying with my backpack on the floor between my, what felt like, styraphome packaged legs. It was nice not worrying about my board getting lost or stolen in transit, though. I guess that's the draw.
So if you've got a skate pack and really want to not lose your board in transit, just never take your board off your bag, run it through the tredmill xray thing like it's a non-issue, and never ask whether or not it's allowed, and most likely there won't be any confrontation about it, unless you struggle to fit your shit in the over-head and clog up traffic while people are trying to seat themselves, anyway.