Unfortunately, many successful attacks on commercial websites are actually attacks on commonly used tools like Plesk. They also leverage the reality that many people who use these "crutches" really don't know what Plesk is actually doing. It really isn't difficult to set up a well-secured server, whether you use mod_perl or CGI. You only need to familiarize yourself with a handful of command-line tools, and SSH and maybe OpenVPN. Tutorials abound.