If automatic transmission had come first, manuals would never be permitted because it takes away attention from driving and is less safe. The only reason anyone considers manuals okay is because they came first and it's baked into our perception that they're a normal way to control a vehicle.

People will say that soon it becomes second nature and you don't have to think about it...and this is mostly true...but it still takes up 'processor cycles' in our brain. More notably, our brains are finicky and can easily shift what they are focusing on and what they are autopiloting.

Personal anecdote: I have a manual because at the time it was the best vehicle I could find that fit my budget, it's only real issue was being manual. I have gotten used to driving it, and it is in fact second nature most of the time. The other day I was at an intersection; the car in front of me went, and my mind focused on the shifting for a moment - my brain decided to put the driving on 'autopilot' instead of the shifting. In that brief moment, when I was more focused on shifting than the road situation, I nearly drove out in front of an oncoming vehicle. Had they not honked I may have failed to notice until a collision occurred.

That distraction could have been any number of things. A wholly undistracted driver is an impossibility. But in this case, it was shifting, something that could have been wholly unnecessary and therefore not been there to distract at all.