You're exactly right, it means to spoon the flour in and then level it off.
If you scoop the flour, meaning you dip the measuring cup into the canister and scoop a large amount out, the pressure compacts more flour into the measuring cup. When you spoon it into the measuring cup instead, the flour is less compact (so there is less of it in the same 1 cup measure). Subtle differences like this can mean a big difference in the end result when baking.
If you were to measure 1 sifted cup, 1 spooned cup, and 1 scooped cup on a food scale you would get three different results (from lightest to heaviest). This is why I'm a big fan of recipes which use weight measurements for the ingredients.