It's not a conscious gesture, it's really just because she's so used to keeping her hands busy that once she successfully gets an arm around his shoulders while they watch the movie she can't quite…keep still. It's mostly just fidgeting at first, until she realizes consciously that she's touching skin. That would be the actual point she tries stroking her thumb along his ear.
She's still…never really sure what to do with her hand, but as long as he won't complain about the gentle touches that are almost absent enough to be excused as unconscious movements…she's probably going to continue to try to get away with them.