If you want the non-IE css to be used, you need to stop it from being commented out:
<!--[if !IE]-->
Non-IE CSS
<!--<![endif]-->
<!--[if IE]>
IE only CSS
<![endif]-->
Notice that <!--[if IE]>
doesn't have a trailing pair of dashes - to any browsers except IE, this will be interpreted as the opening of a comment, which is then closed later by <![endif]-->
.
Conversely, <!--[if !IE]-->
is a standard, self-closing comment (as is <!--<![endif]-->
). Any code between these lines will be processed by any browser except IE.