It is difficult to say what exactly the windmills represent or why the author chose them as the target of Don Quixote's anger. There are two possible explanations for this, both of which are probably true to an extent, so it's up to the reader to choose how to balance their interpretation.

One possible explanation is that the windmills simply look like monsters.

Just then they came in sight of thirty or forty windmills that rise from that plain. And no sooner did Don Quixote see them that he said to his squire, "Fortune is guiding our affairs better than we ourselves could have wished. Do you see over yonder, friend Sancho, thirty or forty hulking giants? I intend to do battle with them and slay them. With their spoils we shall begin to be rich for this is a righteous war and the removal of so foul a brood from off the face of the earth is a service God will bless."

"What giants?" asked Sancho Panza.

"Those you see over there," replied his master, "with their long arms. Some of them have arms well nigh two leagues in length."

"Take care, sir," cried Sancho. "Those over there are not giants but windmills. Those things that seem to be their arms are sails which, when they are whirled around by the wind, turn the millstone."

— Part 1, Chapter VIII.

This is an interesting notion, but the text does not encourage this interpretation.  The essence of the novel is that Quixote, in his deluded state brought on by reading too much Romance literature, sees everything in the real world as some element in the Romantic world. The large size of the windmills, together with their moving "arms," give Quixote the delusion that they are giant foes to be defeated.  While the novel does parody Cervantes' real world, his complaints are not economic or even social, so much as moral and ethical.  Windmills were ubiquitous in Cervantes' time, and there is no evidence that he had any specific complaint against the granaries that used them.  The literary device here is personification, giving human form to inanimate objects.  Quixote also mistakes a prostitute for a high-born lady, but Cervantes is not criticizing the profession; at most  he is lamenting the descent of womanhood from its pedestal in earlier times.  (Having said this, however, let me encourage you to continue making these speculative leaps as you read; they can be fruitful.)