"To a Mouse" takes place in a farmer's field, and it takes the form of an address from the farmer to a mouse that he's just turned out of its nest. Sure, it was an accident, but our farmer-speaker still feels badly about it—and it gives him the opportunity to reflect on the relationship of all of mankind with the natural world. How do you think the mouse feels about this silver lining, though?
The agricultural setting of "To a Mouse" is appropriate, given the poem's description of the injustice of man's "dominion" over nature—nowhere is man's control over nature more evident than in a plowed and cultivated field. So take that, nature.
A mouse is an appropriate subject for this poem because it has enough in common with humans that Burns' readers can sympathize with its plight, but it is also small and relatively helpless. Poor mousie.