jQuery not working in zen theme
It would be helpful to know what version of drupal you are using.

Modifying html.tpl.php to add Javascript like this is really a bad choice as it is a very brittle way of coding something.

Jquery in Drupal 7 is loaded using the noConflict mechanism. This avoids javascript namespace collisions:


  Many JavaScript libraries use $ as a function or variable name, just
  as jQuery does. In jQuery's case, $ is just an alias for jQuery, so
  all functionality is available without using $. If we need to use
  another JavaScript library alongside jQuery, we can return control of
  $ back to the other library with a call to $.noConflict():


If you wanted to use code like you've written you would write:

&lt;script&gt;
    jQuery(document).ready(function() {
        alert('hi');
    });
&lt;/script&gt;


You're better off adding a scripts[] entry into your theme_name.info file and placing such code in its own javascript file in your theme directory. Drupal will load it into the HTML &lt;head&gt; for you and aggregate your javascript files for you if you have aggregation turned on.

# In YOURTHEME.info
scripts[]= js/example.js

/* Example /sites/all/themes/YOURTHEME/js/example.js */
jQuery(document).ready(function($) {
  $('nav ul.primary-menu').append('&lt;div class="nav-blackhole"&gt;&lt;/div&gt;');
});