Creating a sub folder inside a root installation?

I don’t know why you couldn’t access the folder. Maybe you wanna check your .htaccess file first. The default rewrite conditions for apache created by WordPress should include the following two lines, which prevents the redirecting to index.php if a physical file or directory is found.

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d

You could force a redirect with another rewrite condition for your directory, but this should not be necessary.

E.g.

<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_URI} !/store/(.*)$
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule . index.php [L]
</IfModule>