I really doubt unikernels will ever be more than a fad. Hardware isn't a good abstraction layer, because 99% of developers aren't kernel developers.

And sure, a kernel's containment mechanism is subject to exploits. But so are hypervisors. At least if you exploit an application in a (properly made) container, you're just an unprivileged user inside the container. You're not root, in the container or out. If you exploit a unikernel application, you can directly go and target the hypervisor.