SQL Server Transactional Replication over Internet
You have probably read that you are able to deliver the initial snapshot via FTP.  This is covered in Deliver a Snapshot through FTP. 

It is possible to replicate two SQL Servers across a VPN.  This is covered in Publish Data over the Internet Using VPN.

Once the VPN is setup, you should be able to connect and authenticate as though the servers are on a LAN or WAN.

If you have anymore questions please let me know.  I hope this helps.