In your case, no work is done.
Intuitively:
If you want to move a wall, you could push on it and you might use a lot of force. The wall isn't moving, and you are simply "wasting" your energy in your muscles. You are not doing any work of any value.
If you push a balloon you can push it far without any real effort. You might move it a long way but that required no significant strength - that is, no significant force - of you.
That is a way to understand the definition of work:
$$W=\int F \cdot \mathrm{d}x$$
Something has to move and it has to matter, or else we won't call it work nomatter for how long the air pushes on that rock.
As the wind pushes on the rock in your example, then if it cannot move it, actually no energy is wasted from the wind doing the pushing (friction, air compression etc. might still be relevant but not considered here). If a wall as in my examples is fixed to the floor and ceiling, then the floor and ceiling don't spend energy on fixing and holding the wall back while it is being pushed on.
That force is applied is not implying that energy is being spent.
(The human body is a special case since it requires energy of flexing muscle fibers etc. in the body to create a force. A human being is wasting energy while pushing but that is because of movements of stretching and compression within the body and has not got to do with the rock or wall that is being pushed)