Is it safe to upgrade to Yosemite when using VMWare Fusion 6?
The latest version of VMWare 6 is now OK with Yosemite.

Previous versions would not even run if the system was upgraded to Yosemite.

I would recommend upgrading VMWare to the latest version of v6 (currently 6.0.5) first, then upgrading the system to Yosemite. That way, when you boot into the new system, you should not have any problems with VMWare not running.