As the detailed answer above says, this error can be caused by many things.
I had this problem too. My setup was Mac OSX 10.8, using a Vagrant managed VirtualBox VM of Ubuntu 12.04, with MySQL 5.5.34.
I had correctly setup port forwarding in the Vagrant config file. I could telnet to the MySQL instance both from my Mac and from within the VM. So I knew the MySQL daemon was running and reachable. But when I tried to connect over JDBC, I got the "Communications link failure" error.
In my case, the problem was solved by editing the /etc/mysql/my.cnf file. Specifically, I commented out the "#bind-address=127.0.0.1" line.
