I've had the same problem.
Use CSS to hide is not the best solution, because sometimes you want users without JS can see the div.. The cleanest solution is to hide the div with JQuery. But the div is visible about 0.5 seconde, which is problematic if the div is on the top of the page.
In these cases, I use an intermediate solution, without JQuery. This one works and is immediate :
<script>document.write('<style>.js_hidden { display: none; }</style>');</script>
<div class="js_hidden">This div will be hidden for JS users, and visible for non JS users.</div>
Of course, you can still add all the effects you want on the div, JQuery toggle() for example. And you will get the best behaviour possible (imho) :