If it does what you wanted it to when you installed it, it's doing things with your permission. If what it was going to do was clearly and correctly explained during the download or install process, it's doing things with your knowledge.
It's like a motor vehicle. You don't need to know how an internal combustion engine works to be able to give informed consent about driving it, but if it starts rolling away after you park it, you're going to either get it fixed or get a new car.
Who said anything about trusting Microsoft? No piece of software is going to ask you for permission for every single operation it does. Malware is more than just that.