@milo might have a point. WordPress loads jQuery in no-conflict mode.
So this:
$(document).ready(function(){
alert('ready');
});
becomes this:
jQuery(document).ready(function(){
alert('ready');
});
if you want to use $ to not have to refactor your code just pass it to the function:
jQuery(document).ready(function($){
$('.selector').html('this will now work');
});