There are various options, the simplest if it is available to you is reconfigure the server so you can run cgi scripts from the public directory. So you can just do www.mysite.com/home.cgi. Although I would recommend using mod rewrite to allow that to be accessed as www.mysite.com/home which is tidier, preferred by search engines and allows you to change the script type without updating links and creating redirects. For example you could change home.cgi to .html, .shtml, .pl, .fcgi or switch to using Dancer and all your links to www.mysite.com/home can remain unchanged.

If the scripts must be kept in the cgi-bin then I would recommend using mod rewrite. You don't need a .htaccess file for each script you can use a single set of rules. Something like one of the two examples below should work. The first should allow you to use www.mysite.com/home.cgi and the second www.mysite.com/home. These are just basic examples you would need to build upon these to do exactly what you want and protect against unwanted rewrites.

RewriteEngine On
RewriteCond %{REQUEST_URI}  /*.cgi$
RewriteRule (.*) ../cgi-bin/$1 [l]

or

RewriteEngine On
RewriteCond %{SCRIPT_FILENAME} !-f
RewriteCond %{SCRIPT_FILENAME} !-d
RewriteRule (.*) ../cgi-bin/$1.cgi [l]
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