I think they try to find areas that are protected where they can, but it's not possible with all of them. I would think that the ones that are in danger are the dwarves and the Cinderella grouping (if they come out that way again this year). I've seen Peter and Wendy wait under the area where you enter Philharmagic. If the characters for Pete's are out, they'll be in a protective area, the same for the princesses and Mickey and the Aladdin characters. I think these new character areas are to make navigating the rain a little easier so that they can still offer characters during those times.