It's because of the intrinisic difference between nature and man. Man created cyberware and the Matrix, so they don't affect their interaction of a psychosomatically created ability, like the Otaku or Technomancers. They aren't necessarily "magical" because Astral space is a reflection of nature manipulated by man's thought. The Matrix and AR are the opposite: Thoughts given form through manipulation of natural phenomenon.
However, if reading through Canon has taught me one thing, is that the true magic inside the "soul" of man is it's ability to give Names. Once you give something a Name, you've inexorably linked that Name to Definition, and all living things have the ability to manipulate Definition. The manipulation of Astral Space and mana are not necessarily the highest forms of Magic, but rather the highest form of Magic is to attribute power to a Name through events and karma. For example, at first the Dunklezahn Rift was unstable but, as people grew accustomed to it, giving it a Name (The Dunklezahn Rift) it became more stable as it's nature was fleshed out. The same applies Somatic Links in Ritual Sorcery, close personal attachment to a Named object, gives it Definition and in that Definition is a pointer that links to the Namer of that Object and the person/thing that gave it Definition.
How does this apply to the Matrix, you ask? By nature, calling the Matrix, the Matrix, gives it a Definition, and so makes the Matrix a Named thing, even if it only exists metaphorically. The Otaku and Technomancers, especially the young ones, are too young and the Matrix begins to Define them, giving them an inexorable link to it and the ability to manipulate it. However, as the Otaku grow, they find that the Definition of the Matrix diverges from the one they've made for themselves by growing up and so they Fade. The Technomancers trapped inside the Matrix were essentially separated from their body and became the Matrix, momentarily assuming the Definition of the Matrix itself, and so, developed the ability to manipulate it without being "in contact" with it.
Otaku are not Magical in the Sense of being able to manipulate Mana but rather they are somatically linked to the Matrix (essentially an artificial Metaplane) just as a mercenary is somatically linked to his favorite gun, or a rigger his favorite vehicle. These connections are not one-way, and if given the ability, the Named objects can affect the Otaku, mercenary, or rigger. A prime example of this is when the Matrix spawns an intelligence, be it an AI or Free Daemon, and can then create it's own Otaku.
Perhaps, if anyone had considered this, one would know that the greatest way to destroy an AI that creates Otaku is to "ritually attack" the AI through its link with its own Otaku.
