I ran into the same issue a few weeks back. You don't need to use tinymce as a jQuery plugin but the option is there if you would like to. The vast majority of the tinymce source code is in the tinymce.min.js file and the jQuery.tinymce.min file just contains the code that wraps the tinymce functionality into a jQuery plugin. Anyways, if you want to use it you'll need to require both.
<script src="/js/jquery-1.10.2.js" type="text/javascript"></script>
<script src="/js/tinymce/tinymce.min.js" type="text/javascript"></script>
<script src="/js/tinymce/jquery.tinymce.min.js" type="text/javascript"></script>
The only main difference as far as I know in terms of TinyMCE is the way the editor is initialised. If you're not using jQuery you'd initialise it something like this:
tinymce.init({
selector: 'textarea',
theme: "modern"
...
})
Whereas when you're using it as a jQuery plugin you can use jQuery to initialise it and you get the added benefit of being able to chain additional jQuery goodness onto your initialisation method. As in:
$('textarea').html('<p>some dynamic content</p>').tinymce({
theme: "modern",
...
})
Other than that they're basically the same I think.