I don't think kernels are inherently less secure than hypervisors, but as they stand, current hypervisor implementations have a better security track record than kernels. The basic point that I am trying to make is that both hypervisors and kernels are just pieces of software meant for partitioning and sharing hardware. Software that has simpler and smaller interfaces also has a lower probability of having bugs that lead to vulnerabilities. I agree that that there are better hardware partitioning implementations out there but unfortunately they are not so popular. I am looking forward to having formally verified kernels like seL4 become more popular.