Jay, many things are very much a matter of scale, or degree. As has been pointed out, there are many creatures living in our soil, if we have good healthy soil, that are actively digging through it. Our plants are sending their roots down, pushing through the soil (daikon is also known as "tillage radish" because of the way its tap root pushes down deep into the soil, right?).
It is not that the soil should be absolutely undisturbed. Indeed, that would be bad, as it would mean none of the various organisms that ought to be there pushing the soil around were there doing their jobs.
It is the case that man has a bad habit of overdoing things - like turning the soil over again and again. It dries out, organic matter oxidizes, the wind erodes the topsoil. Lots of bad things can happen to
land that is repeatedly tilled. And even conventional large scale agriculture has been catching on to the "no-till" idea.
But, there are plenty of seeds that need to actually be put in the ground, not just broadcast over it - so you have to do a little disturbance there. Occasionally you have a weed that needs to be pulled, so there's a little disturbance there. Sometimes you have root crops, that have been pushing the soil around forming their tubers or tap roots that you will need to disturb the ground a bit more to harvest them.
As long as you are not turning over the soil over a large area, it is not a big destructive thing. Disturbance creates opportunity as well as disruption. Taking out the potato makes room for something else to grow there, and the bit of soil churning may bring the seeds of something else to a place where they can germinate. And that may translate into you having weeds in your garden - or it may mean that last year's lettuce seed that had self-sown now gets a chance to grow.