Try:
RewriteEngine On
RewriteCond %{HTTP_HOST} !^www\. [NC]
RewriteCond %{HTTP_HOST} ^([^.]+)\.domain\.com$ [NC]
RewriteCond %{DOCUMENT_ROOT}/%1 !-d
RewriteRule ^ - [L,R=404]
RewriteCond %{HTTP_HOST} !^www\. [NC]
RewriteCond %{HTTP_HOST} ^([^.]+)\.domain\.com$ [NC]
RewriteCond %{DOCUMENT_ROOT}/%1 -d
RewriteCond %{DOCUMENT_ROOT}/%1%{REQUEST_FILENAME} -f [OR]
RewriteCond %{DOCUMENT_ROOT}/%1%{REQUEST_FILENAME} -d
RewriteRule ^(.*)$ /%1/$1 [L]
in the htaccess file in the domain.com
's document root.