It's important to note that the blog post doesn't mean, "Linux is done for," but rather, "Linux is going to be a different kind of system than it has been historically." Some people think this is a good thing, and some think it is not. EDIT: I want to emphasize that I am trying to write this comment neutrally, not endorsing either side, so while my biases may sneak in, my intention is to be fair to both sides. Both sides have arguments in their favour, and I'd hope people consider both before coming to a conclusion.
All Unix-based systems start by running a single process known as 'init' which is responsible for setting up the system, starting all other programs, and managing various services as they run. The change under contention is the widespread inclusion of a relatively new piece of software called systemd, which replaces the historically popular sysvinit, Ubuntu's alternative known as upstart, and various other competing systems. All of these are different approaches to building an init system.
In contrast to some of the other systems, systemd is written less in terms of traditional Unix-style tools (like pipes and plain text files for storage), choosing instead to build on newer and more elaborate communication interfaces and store in specially designed binary formats. Systemd consists of a large family of interrelated pieces of software, many of which are nominally optional but generally expect to be used together. One point of contention is whether systemd is "too large", as proponents argue that developing these pieces together will increase their quality, while detractors argue that this makes it too difficult to substitute components if necessary and that these pieces should not be part of the same conceptual package.
Additionally, the architectural choices of a large, widely-used package integral to the functioning of a running system will influence the design and assumptions of other pieces of software and even Linux itself. Already, the Linux kernel has incorporated the newer communication systems used by systemd into the operating system itself (the mentioned KDBus), which many believe to be a sign that the inclusion of systemd will change the way that Linux operates and the way programs expect to interact with the kernel and with each other.
An important factor here, whether good or bad, is that these choices make Linux into a very different system than it has been historically, and very different than other Unix variants. Proponents argue that this is a step forward, as the facilities offered by Linux historically might not be appropriate tools for the current uses of Linux. Detractors disagree. Either way, the conclusion is that systemd is a change in the way the operating system is structured and used which has been a major point of contention in some communities.