In order to redirect all requests for www.yourdomain.com to yourdomain.com, you should set the appropriate rewrite rule. This can be done by adding the following lines at the beginning of the .htaccess file in your public_html folder:

RewriteCond %{HTTP_HOST} ^www.yourdomain.com [NC]
RewriteRule ^(.*)$ http://yourdomain.com/$1 [L,R=301]

From now on, when someone accesses http://www.yourdomain.com s/he will be redirected to http://yourdomain.com.

Using this method is safe because it should not create any redirection loops nor it should interfere with other rewrite rules.