tl;dr

The CPUID instruction takes a lot longer to execute in a VM than it does on bare-metal so we can measure it and confidently say if we are running inside of a VM or not. It is possible because a VM will need to call a VMEXIT to let the VMM execute the instruction bare-metal (and that takes time) or in case of emulators, it needs to manually move the data into the virtual registers (and that also takes time).