As MJ and Ssd says it takes a while, with me it's been a looooong while , I've got about 800 hours now and recently done my Instrument rating and will be sitting my commercial check ride in a few weeks and am only now thinking this flying thing is clicking and feeling comfortable (hopefully not complacent)with the whole thing.
Being a farm boy I would describe it as the feeling I got in my teens when backing a grain trailer into a shed, or burling the tractor down the right tattie drill or other tractor driving tasks without having to think about it or demolishing stuff , it becomes second nature.