Really wouldn't recommend using IIS FTP in Windows Server 2003, it's very poor and a pretty big security risk. Recommend you look at either FileZilla Server (If you're dead set on FTP) or look at SSH which would be better security. FileZilla can ratelimit out of the box and block repeated attacks, plus you can change the ports easier than the inbuilt IIS FTP Server. Externally I change the SSH port or FTP port to something in the 4000+ to 5000 range just to reduce the attack vector.
If you're REALLY wanting to do this you can change the home folder the FTP server points to, to the WWWROOT folder. Depends on access and file permissions of your IISUser.