I’m glad you asked! I had the exact same first impression when I started: the game just played itself, so why did it need me? I found my answer in this thread in the Matrix forums, five years ago:
It suggests immediately going to options and switching most or all systems to “suggest” rather than “auto”. This means that the game will prompt you to make decisions rather than automating them for you. Once you get more accustomed to things, you can switch everything to manual. I followed this advice, but I left a few things on automate to make things easier for myself. I also followed the rather detailed tutorial the thread offers; it helped me a lot.
Being five years old, that thread may be somewhat dated now? I’ll have to fire the game up to see. But discovering how to change the automation settings made all the difference to me.