Web servers often have a cgi-bin/ directory at the base of their directory tree to hold executable files called with CGI. A cgi-bin is a special directory designated in the configuration files of a web server to allow execution of CGI scripts in specified directories. Many new servers have done away with this and allow users execute any scripts ending in .cgi.
The cgi-bin/ remains as a default folder on all new accounts. This is simply to remain compatible with older scripts. If you do not intend to use the cgi-bin, it can be deleted without any problem. It can be easily re-created as well, just by re-making the directory.