Anyone with knowledge of how to submit a charge to your credit card company could have done it. Why $100? Because that's what the thieves decided.
And Apple can do nothing if the fradulent charges aren't coming through them, which if they aren't showing in your Purchase History probably aren't (in which case removing your card information from your iTunes Store account will do no good, since the thieves haven't cracked your iTunes Store account). It could just have easily been faked to be your grocery store, or Amazon, or any other merchant. The thieves probably chose the iTunes Store since 1) it's popular and 2) for many users the iTunes Store carries a lot of traffic and so additional charges may not be noticed.
Again, this is the problem of your credit card company to follow up on. They probably will need (and offer) to issue you a new card.
Regards.