From a technical perspective, there's no reason at all. In fact, some webservers allow you to have your CGI scripts (which don't necessarily have to be written in Perl) on another machine.

The primary reason most people separate it is to have a separation of concerns - you don't want your business logic mixed in with your display logic.

The other reason most commonly cited is that it's easier to lock down your cgi-bin directory than it is your htdocs directory. So, there's a small security gain, but not a lot.