I'm aware of the common misunderstanding about action and reaction canceling each other; they don't because they don't act on the same object. This is about a more subtle issue: exactly where is the work being done? Consider a bicycle wheel:
The bike wheel pushes the earth backwards (action force $F_A$) and the reaction force $F_R$ is in the opposite direction on the bike wheel (ignoring gravity). But the point of the wheel that touches the ground is not moving relative to the ground; therefore, neither the reaction force nor the action force does any work; therefore, this force cannot be what causes the bike to accerelate from a standstill. (If you account for the displacement of the earth, there would be on the order of $10^{-20}$ W of work, which is small enough to ignore.)
The chain of the bike definitely does work on the sprocket on the back axle (teeth and chain are moving with a force). Presumably, the axle does work on the bike frame; the frame and rider are pushed from the axle. Something tricky happens between the axle and the tire.
The question is: what is a clean way to describe the forces (especially those acting on the wheel) so that this is all consistent? Is it possible to draw the relevant force vectors in a free body diagram?
Edit: to make the problem more well-defined: the bike is accelerating, ignore air resistance, and ignore gravity (you can pretend that it's a rack and pinion construction that works without vertical force.
Here is a diagram with the forces around the sprocket/chain and the forces around the road contact point (arrows not on scale). How do you describe acceleration?