That's only true when the OS's in question require different kernels. For OpenVz/Virtuozzo for example their RHEL based kernel has long been the preferred one for a lot of people for non-Redhat Linux versions too.
I agree with you there are still lots of reasons people will want VM's though.
We've picked containers at work, but only because while we host customer sites, we run and manage all of them, and so have a lot of flexibility a typical hosting provider doesn't have.