Now I understand the misunderstanding here. I'm fine with protecting everything by user-chosen permissions. As long as the end user has full control over them, file permissions, access control lists, and fine-grained internet controls are perfectly fine. My operating system has all of that. What I rigorously reject is when the makers of an operating system restrict access without giving the end user full control over everything. That should in my opinion be prohibited. The user's full control must also be easy to exert to prevent malicious compliance.
So maybe I misunderstood you and there is no disagreement at all. Of course, I think file permissions and protected memory can make sense.