For skies of couple-colour as a brinded cow; (line 2)
The natural landscape in "Pied Beauty" is oriented around agriculture. Hopkins has farming on the brain, as with this comparison of the sky to a cow. That's a little like saying, "That waterfall looks like bales of hay falling off a cliff." Notice how Hopkins looks at the positive ways in which humans interact with nature. He could have written about the ways in which humans have harmed nature, but clearly did not have this theme in mind when writing this poem. Check out "God's Grandeur" to read Hopkins's version of the darker side of human interaction in nature.
For rose-moles all in stipple upon trout that swim; Fresh-firecoal chestnut-falls; finches' wings; (lines 3-4)
Hopkins subtly mixes references to human activity with his descriptions of nature. The chestnuts are compared to the coals in a fireplace.
Landscape plotted and pieced--fold, fallow, and plough; (line 5)
The landscape was always so "pied." Humans have divided up the countryside into "plots" and "pieces" for farming different crops. Hopkins considers this process to be natural.