How to get rid of the username of registration form in theme my login wp plugin?

You are not trying to remove it by WordPress, but by jQUery.

It looks more a problem matching the element you want to hide.

I don’t know your ids and classes on your html to give you the exactly answer, but the a simple proccess to find your answer:

You can open your console developer (Chrome) or firebug (Firefox) on your navigator to insert your function on javascript console:

jQuery(document).ready(function( $ ){
    $("#registerform #user_login, #your-profile #user_login, #your-profile #nickname, #your-profile #display_name, #your-profile #url,  #your-profile #description").parents("div.form-group").hide();
});

and modify until it matches and hide what you want. The Console developer also helps you you find the id and or class name you want to hide.

So you get the right function and replace in your function:

function prefix_hide_personal_options() {
?>
<script type="text/javascript">
   *** here ***
</script>
<?php
}