Presumably this doesn't help protect their identity, since they are also accessible over the regular Internet. Does it make things somehow easier for users? I think you have to set up a local Tor client in either case. Is there a security benefit?
This allows communications between the client and server to exist entirely within the Tor network (no exit node needed). For sites that are not using SSL the primary benefit of doing this is end to end encryption. For sites which use SSL it can prevent many types of attack, or prevent traffic which uses a cipher suite which does not support perfect forward secrecy from being recorded and deciphered in the future (assuming Tor's encryption can't be broken in the future, but if they're using a future attack on SSL this may not be a good assumption).