When I place a htaccess file in a customer doc root it works ok until I add any content to it then I get a 500 internal server error. Here is a sample of what is in the htaccess file:

RewriteEngine On
RewriteCond $1 !^(index\.php|assets|downloads|robots\.txt)
RewriteRule ^(.*)$ /index.php/$1 [L]

Im using fcgid and here is the vhost conf file:

  ServerName ************.uk
  ServerAlias *.**************.uk
  ServerAdmin ********@gmx.com
  DocumentRoot "/var/customers/webs/********/"
  FcgidIdleTimeout 30
  SuexecUserGroup "*******" "********"
  <Directory "/var/customers/webs/*******/">
    <FilesMatch "\.(php)$">
      SetHandler fcgid-script
      FcgidWrapper /var/www/php-fcgi-scripts/********/**********.uk/php-fcgi-starter .php
      Options +ExecCGI
    </FilesMatch>
    Order allow,deny
    allow from all
  </Directory>
  ErrorLog "/var/customers/logs/*******-error.log"
  CustomLog "/var/customers/logs/******-access.log" combined

Any ideas?

i would guess wrong user:group of the files.. But please post your error_log ans suexec_log

Or you have errors in your .htaccess