This is actually the directory outline:

/
/css
/js
/admin
/config
/etc...

Making this what I'd like:

/                      <-- Mod re-write for this directory only, skip the rest
/css
/js
/admin
/config
/etc...

.htaccess file:

# Turn rewrite engine on
RewriteEngine On

# Set the base path
RewriteBase   /

#  now the rewriting rules
RewriteRule ^([0-9A-Za-z]+)/?$ /query.php?id=$1 [L]

Want to skip all sites except the main directory, how do you do that?

Another solution: Put one of these simple rules before your rules:

RewriteRule ^(css|js|admin|config|…)(/|$) - [L]

RewriteCond %{DOCUMENT_ROOT}$0 -d
RewriteRule ^[^/]+ - [L]

The final named rule is useful for any existing directory but only when put into the .htaccess file within the document cause of the server. Otherwise you will have to adjust the RewriteCond expression %{DOCUMENT_ROOT}$0 using the specific path, e.g. %{DOCUMENT_ROOT}foo/bar/$0.

Perhaps you have attempted to place b .htaccess file in each and every sub-directory with "RewriteEngine Off"?

(Maybe this can be a question for serverfault.com)