Yes. It is a skull. There is an easy, and obvious explanation for this...
You see, there's a purpose to Mario's sliding down the flag pole. When he gets down, he takes down the flag. When someone takes down a flag, it usually means they are taking down an enemy's flag, and liberating/capturing the stronghold. In this case, Bowser and his troops put up the skull flags, which are theirs obviously, but when Mario gets through the level, he is taking down their flag and liberating the castle, which is the stronghold. I once thought it was a Mushroom or a Peace Symbol, because it was next to the Toads' castle, but I wondered why Mario was taking it down, since he was a good guy, but I figured this out eventually. (Heh, when I was like 8) Anyway, there's your explanation, straight from Me, the Mario Genius.
I am Meowrik! The 5th Samurai Pizza Cat! beware the fearsome fury of my fiery Jalapeno Katana!