If you have control over the servers, the easiest way to secure the connectivity between the MySQL server and the web server is to put a 2nd NIC card in each server.
Then, run a cross-over cable between the two. Use non-routable IPs on this connection. Now, the MySQL server can only communicate with the web server, unless you enable IP-Masquerading on the web server.
This is very secure and requires no additional layers of software encryption to slow things down on a busy system, of course you have the cost of 2 additional network cards and a cross-over cable.
Hope this helps.
-Rich