When using JCE Editor (let's admit, we all do), you will find yourself in trouble sometimes, as JCE will be cleaning up your HTML code and clear iframe code, even if you have followed the steps in how to allow YouTube videos in Joomla articles which describes, how to configure Joomla to allow code inserted in articles.
To set up JCE Editor to allow iframes, go like this at first:
The second step to take to disable JCE deleting iframe code:
An image to display JCE Editor settings at Components -> JCE Administration - > Editor profiles -> Default -> Plugin Parameters -> Media support
Here is a video added with JCE and with iframes from YouTube: