I've never had a hotel charge me for early check-in and I often show up a few hours early (sometimes before noon). I agree that they probably thought you wanted a guaranteed early check-in, which they would charge for (although $99 seems like a bit much, but I guess it depends on the hotel, room type, etc.). Hopefully it isn't the start of a new fee trend. I'd just go to the desk when you arrive, acknowledge that you are early and politely ask if there are any rooms ready. If not, they'll store your bags and call you when the room is ready.