I just learned that VM Ware doesn't recommend backing up the Virtual Machine to Time Machine. Unfortunately, it's too late: my 1Tb Time Machine drive is full, in less than two months. When I try to delete the numerous copies of the VM from the Time Machine drive, a message pops up to tell me that backups cannot be deleted. Does anyone know a way around this?
What does this really have to do with VMware Fusion? Nothing! In other words Time Machine is a part of Mac OS X not VMware Fusion and VMware Fusion has absolutely no control whatsoever over your issue.
The first thing I'd do is to exclude the Virtual Machines folder from Time Machine. You can click the ? button in the lower right corner of the Time Machine preferences window to see how that's done or just click the Options button.
How are you trying to delete the files from the Time Machine backup are you going through Time Machine or directly to the Backups.backupdb folder on your Time Machine backup disk? If the later try the former as one is not supposed to do it by the latter method.
Have a look at "Removing a file from your backup disk" in Mac Help.