UPDATE: At the time of this posting (2013) my team was still having to test for IE6 and IE7 so, hopefully, it will not be relevant for anyone reading it now. But just in case:
Compatibility mode in IE was — to my understanding — meant to allow obsolete web applications to render correctly by simulating an outdated version of the browser. For an ordinary person this option should not be set by default, however, some larger organizations that distribute hundreds of computers at a time may have it chosen as part of the profile they imprint on each system.
Nonetheless, there is a way to protect your CSS3 and HTML5 from compatibility mode! Just put this additional meta tag in your <head> before the other meta tags and it will disable compatibility mode as an option when people visit your site using IE by forcing it to use its most current rendering engine:
<meta http-equiv="X-UA-Compatible" content="IE=edge">