Docker may be a fad, but containers are not. Containers are essentially just 3 things:
1) A set of linux namespaces (a pid namespace, a mount namespace, etc)
2) A set of cgroups
3) a chroot to a virtual file system
It's not a virtualization technology, so it doesn't have run-time overhead. If your OS is Linux, the "dockerized" application is a native process that you can see when you run ps. You can do the exact same thing that Docker does if you know a few system calls to create the namespace, cgroup and chroot on the fly. Docker just puts it all together so you don't have to. Every Linux process technically runs in a container, they just share the 'global' container rather than getting their own. There's nothing magical about Docker, except that you don't have to be a Linux guru to take advantage of native Linux features. So the "fad" that is containers will not go away until Linux experiences a massive design shift. Sure, Docker may fall out of fashion as the tool for creating containers. If you want a more timeless skill, learn how to create namespaces and cgroups yourself.
As far as the oft-repeated complaint that Docker runs as root, this doesn't have to be an issue. Docker starts and stops processes (it calls them containers, but they are native processes). Those containers/processes do NOT have to run as root. So complaining that the Docker daemon has root access is really no different than complaining that systemd has root access. They both manage processes for several users and therefore require root access. Configuring either also requires root access, but none of the processes they spawn need root.
If you have half an hour to burn, here's a session from DockerCon 2017 where the presenter writes a program that creates containers. It's kind of like a rudimentary Docker. If you like the idea of process isolation but aren't comfortable with a faddish tool like Docker, she walks you through what Docker is actually doing under the hood. You can incorporate any of the ideas you like into your existing deployment strategy and ignore the rest.
https://ancillary-proxy.atarimworker.io?url=https%3A%2F%2Fwww.youtube.com%2Fwatch%3F...