Route53 Private Hosted Zones allow you to setup private domain names that can only be accessed from within your VPC.
These private domain names can then be used for various purposes, for example accessing the database through such a private domain name. This way if you need to change the database you just need to change the CNAME to a new database and your application works without any code change.
There is also a security advantage because the domain name is accessible only from the VPC and if your database credentials are leaked the potential attacker still cannot access your database through the private domain name.
