I think that it might be because the skycam doesn't show any (or will show only a few) of the advertisements on the side of the pitch, which (on their electronic monitors) change every 30 seconds or so. Since the World Cup doesn't have any commercial breaks (save for half-time, and the stretch between game and overtime), I imagine that the advertisement space for these sides (especially on the side facing the "traditional" camera shots) are quite expensive. Therefore, I would imagine that the use of the skycam would be discouraged on the grounds of commercial reasons.
However, after consulting the Oracle of Google, I found this more practical conjecture posted on Core77:
Skycam use in the World Cup has been far more sparing, presumably because the unpredictable direction-changes and flight arcs of a soccer ball mean the camera must be safely out of the way; you mostly see it in use during set pieces, behind the action.I suppose that the generally-one-direction nature of American Football does make it a much better sport with which to use this technology. Of course, if there were some way of putting a transponder on the soccer ball so that the skycam would automatically follow the ball (saving the viewer from the cameraman's inevitable jerkiness on sudden changes in direction), that would be an innovative way of watching the game.