The hens rebel because Napoleon took their eggs to sell to the humans.
In Old Major’s speech, one of the things he calls attention to is the fact that the hens have to give up their eggs. He uses this as an example in his long litany of abuses of the humans.
And you hens, how many eggs have you laid in this last year, and how many of those eggs ever hatched into chickens? The rest have all gone to market to bring in money for Jones and his men. (Ch. 1)
Old Major paints a picture of a world where animals are not enslaved to humans. This is the dream that he predicts for Animal Farm. The animals will run the farm and look out for each other. No animal will exploit any other in this idealistic vision of the farm.
Things do not turn out the way Old Major predicts. When the animals oust the humans, the pigs end up in charge. They play the role the humans would have. Eventually they end up exploiting all other animals just the way the people did. They do this slowly, before the animals really realize what is happening. When Napoleon runs Snowball off, the last idealism is gone.
Things do not go well for the hens from the beginning. When they suggest that Jones used to give them milk in their mash, Napoleon tells them to forget about the milk. The pigs are using it for themselves, and suggesting to the other animals that they deserve the milk and apples because they are the brains of the farm.
The hens still do their part on the farm. Even though they are small and have nothing that can be used as hands, the hens help by gathering the last bits of straw so that none is wasted. The hens are described as among the “stupider animals” who cannot learn the Seven Commandments (Ch. 3). The first time Napoleon betrays them is when he makes an arrangement to sell their eggs.
He was therefore making arrangements to sell a stack of hay and part of the current year's wheat crop, and later on, if more money were needed, it would have to be made up by the sale of eggs, for which there was always a market in Willingdon. The hens, said Napoleon, should welcome this sacrifice as their own special contribution towards the building of the windmill. (Ch. 6)
It makes the animals uneasy to trade with humans, because this was something they had vowed not to do. Taking the hens’ eggs is like stealing their children. It was something the humans had done without thinking, but they did not think the animals in charge would. When Napoleon demands that the hens give up their eggs, they are not happy about it.
When the hens heard this, they raised a terrible outcry. They had been warned earlier that this sacrifice might be necessary, but had not believed that it would really happen. They were just getting their clutches ready for the spring sitting, and they protested that to take the eggs away now was murder. (Ch. 7)
The hen uprising is the first hint of rebellion at Animal Farm. Rather than give up their eggs to be sold to the humans, the hens drop them so that they are “smashed to pieces on the floor” (Ch. 7). In response, Napoleon orders the hens’ rations stopped until they give in. The pigs tell the animals that the nine hens that died were killed by “coccidiosis.” Soon this leads to mass confessions, in which “three hens who had been the ringleaders in the attempted rebellion over the eggs now came forward and stated that Snowball had appeared to them in a dream and incited them to disobey Napoleon's orders” (Ch. 7). They are executed. Sheep also confess to being in league with snowball.
The story of the hen rebellion is an example of how the lowest class of society is exploited but cannot stand up to the pressure. This is why the hens confess, and the sheep too. They are both considered the dumbest animals on the farm. They succumb to Napoleon’s propaganda even if they do not understand what is going on.