A FastPass for Fantasmic! doesn't really let you skip the line, it just lets you sit in the FP half of the theater. The seats toward the front will still fill up first, so if you get there late, you may find that the best seats are still taken. You can though just go to the non-FP side if you find the seats are better over there, as I believe they seat FP holders first.
Fantasmic! is not really worth the FP in my opinion. You can get it as an in-park FP after your first 3 (they are usually easy to get since there are so many).