I take it your sister had the mother when the mother birthed the kitten. Were there any other kittens in the litter? If so, how are those other kittens doing? Having lots of human contact at a young age is the best way to make a cat comfortable around humans.
How do you know that the kitten is scared, instead of just a cat that loves to sleep under things?
I mean, if your sister was doing something wrong with the kitten, then she should stop doing whatever that wrong things was. Without knowing anything else, I'm personally hard pressed to come up with any other advice.
However, I do have advice for shy kittens that didn't get enough human contact when they were really, really young. We adopted my two cats and their mother when the kittens were something around a month old (a neighborhood stray who came out looking for food once she could leave her kittens a little bit). The kittens did not like us. Now, after reading a lot of stuff on this board, I figure I should have been more interventionist in touching them. But what I did was just feed them and play with them (use an interactive toy; I used yarn, but it can be a serious swallowing hazard, so if it's used it must be very religiously put away in a completely cat-impregnable place). With my very hands-off (except for playing) method it took about 4 months to get two of them to be friendly, and about a year to get another one friendly. The one that took a year to be friendly with me is only now (she's 4) occasionally letting any human being other than me touch her. And there was absolutely no forced contact in her life (unless it happened when no-one I ever heard about knew they were under a house, and excepting a few vet visits) that could be blamed on her shyness. She just didn't have enough human contact early on, and she's just suspicious in nature.