Depending on what you want here are two suggestions.
Example 1
Is very simple if your site is called with just it's url this
will send it to your sub directory.
Copy this text and save as index.html and place it in the root of your url.
(1)
Code:
<html>
<body onload=location.replace('http://www.yoursite.com/store/index.php')>
</body>
</html>
Example 2
Is a rewrite mod that you would need to be place in your root .htaccess file
This rewrite works alot different then most. It allows you to have a
sub directory with your zen cart in it but when looking at the url address in a browser
it will display the store as if you have it in the root.
(2)
Code:
Options -Indexes
RewriteEngine on
Options +FollowSymLinks
RewriteCond %{HTTP_HOST} !^www\.yoursite\.com$ [NC]
RewriteRule .* http://www.yoursite.com/ [L,R=301]
RewriteRule ^$ store/index.php [L]
RewriteCond %{DOCUMENT_ROOT}/store%{REQUEST_URI} -f
RewriteRule .* store/$0 [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule .* store/index.php?q=$0 [QSA]
You will need to edit the urls of these examples to fit your needs.