Yep, FB has hit the nail on the head (pun intended). Cotter pins are a taper fit, and like most tapers need a blow to distort the taper to break the cold weld that occurs between the two surfaces. Either his pipe method or hold a big hammer (at least twice as heavy as the swinging hammer) next to the head of the pin while you hit the other end of the pin. In the old days we'd just slightly loosen the nut to leave a small gap between the nut and the crank so the thread wouldn't get mushroomed and we could use the pin again. If you do it right you won't mark the crank at all.
If you are using the c-clamp method get the clamp really tight then give a whack with a hammer on the end that's pressing on the pin.