That's the point of VMWare, so you can virtualize another system inside of your primary one, in effect "sandboxing" the guest OS so you don't screw anything up.
Running an OS in a VM per se is unlikely to. But if the host system has poor package management and the virtualization software proves problematic (some of them install files all over the place, including kernel extensions), restoring the host system to its previous state can be difficult. It's not an unreasonable concern.