Encryption is trivial with modern libraries: the hard part is securing the key(s).
So you need to look at what you're trying to secure, and what threats you are trying to secure against.
To encrypt a file so only the current user can see it on a client workstation, File.Encrypt is a good choice, or DPAPI with the CurrentUser scope.
For a configuration file on a single server, DPAPI using the LocalMachine scope is a good choice. You then need to make sure only authorized users are able to log in to the server. Here you're essentially delegating key management to Windows.
For a configuration file on a server farm, you need to share the key between the servers. RsaProtectedConfigurationProvide is a good choice, but you have more work ensuring that all servers have access to the same key, and that it is protected against unauthorized access (e.g. using a DACL).