A very good point by posters above - many dogs feel safe in their crate and it's important that they have this safe place, whether it's a crate or a bed or something similar.
Sam still goes into his crate when we are leaving the house. We don't close the door anymore though. He's been free to roam the house when we are gone since he was around a year old. The poor guy is terrified of thunderstorms and "hides" in his crate if a storm comes up and we aren't here. Poor baby!