I think that Clover and Boxer are shown in positive lights because they are the most honorable characters in the story. At a point where so many of the animals are motivated by different ends, Boxer and Clover are really only concerned with the betterment for all animals. They are more worthy of embodying the tenets of Animalism than any other animal. Consider the opening scene, where both of them are concerned with not stepping on the other, smaller animals. Clover is protecting the lost ducklings, as more important than anything else. While the other animals are fighting for positioning in the front of Old Major's speech or driven with excluding other animals in the new world order, Boxer and Clover are only concerned with all of the animals having a better life. Boxer represents this in how tirelessly he works for the farm, waking up earlier and earlier to get more work done, and mourning when he kills a human being in the Battle of the Cowshed. Clover struggles to find meaning after Napoleon's savage display, seeking to reconstruct meaning, and Boxer continues to "work harder" in the name of "Napoleon is always right." Orwell has little choice to present these two horses in a positive light because they don't do anything worthy of criticism. Even if one wanted to say that a fault of their was being too trusting of authority, it is difficult to go very far in criticizing them for doing so because it is a reflection of their heart, and their state of being. It is reflective of how much the power of inclusion and care for all are tenets that make people honorable and better than most, but also makes them more susceptible to being manipulated by those in the position of power. It is for this reason that Orwell shows them in positive lights.
If you noticed, George Orwell made boxer out as a very hardworking and loyal animal. What George Orwell is probably trying to say is that boxer represents the gullible people of the communist country, woking their whole lives for their leader and so called "comrade" and not earning anything.
Thanks for the answer. I also thought maybe Orwell wants us to sympathize with the polterait, or maybe he wants us to provide a comparison between the kindness of the horses and the tyranny of the pigs?