setfont modifies the font in the VGA console (what you get when you press CTRL-ALT-F1, etc) It won’t do anything in Terminal.
Normally only the root user can access the console device that setfont needs to connect to in order to make the font change. This is why you get an error message when you run it from your normal user account. An exception is when a user is logged into the VGA console… then the user has access to the console and setfont succeeds.
The fact that you get the error message whenever you start Terminal, means that you likely have some command in your .bashrc, .bash_profile, .bash_login, .profile or /etc/profile that is run whenever you start a terminal. Could it be that you have setfont in one of these places? otherwise, look for something else that may be accessing the console.
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