Deploy each mongod instance on a separate physical host. If you are using VMs, make sure that they map to different underlying physical hosts. Use the bind_ip option to make sure that your server maps to a specific network interface and port address.

Use firewalls to block access to any other port and/or only allow access between application servers and MongoDB servers. Even better, set up a VPN so that your servers communicate with each other in a secure, encrypted fashion.