How do I prevent Chrome going fullscreen while playing youtube videos?
Chrome takes you into a fullscreen window when you try to play a HTML5 video in fullscreen. On YouTube, if you are using the HTML5 preview/beta instead of the standard Flash (or if you have uninstalled or never installed Flash on your computer), that will continue to happen.

For YouTube at least, make sure Flash is installed and drop out of the HTML5 beta program. This is only a short-term solution, and only applies to video sites that still use Flash.

Try that and see if it work.