This is one of the many cases where most filters fail miserably. I'm one of the developers for the Clean Speak products from Inversoft. Our filter is the best one available. It is intelligent enough not to think that cases like "won't it" are profanity. It also handles a ton of other cases. We figure, if you are going to have a profanity filter, it might as well be as smart as possible so that the players don't get annoyed by it.
Star Trek online should consider using our filter for their game. It's used in a number of other games and virtual worlds.