Security is a big reason to use VMs. Containers share the kernel with the host. That means that any of the kernel vulnerabilities from this year (like DirtyFrag and CopyFail) could have been used to compromise your host. Once the host is compromised, the only way to be safe is to literally buy a new machine. Seriously. Viruses can bury deep and even infect the motherboard firmware to persist indefinitely.

Kernel vulnerabilities are frequent enough that I find VMs worth it. I still use containers in my VMs though.