Which distribution do you have. Linux uses Pluggable Authentication Modules to control that sort of thing. Its possible that if the policy is set to allow root login that the securetty file isn't referenced. But I'm just guessing.
Here are the first two lines of my /etc/pam.d/login file:
auth required pam_securetty.so
Your distribution probably has a place to change the root login policy, which will save you from having to setup the /etc/pam.d/ entries yourself. In Mandrake Linux you go to MCC -> Security -> Levels and Checks -> System Options Tab. There you can disallow remote root login, or even direct root login.
I'm sure your distro has a similar tool.
Not allowing root log-in is a good idea if there is more then one person with root access. Then when ever something is done as root, you can tell from the logs which root-user made the change by checking who su-ed to root , and you know who to ask if you have any questions.