The protagonist of Never Let Me Go at one point mentions that while she was growing up in Hailsham, she and her fellow students were never really sat down and told what was planned for their futures, but instead gradually allowed to hear bits and pieces of information a little at a time, or told about things when they were just slightly too young to understand, so that by the time they did understand it, the knowledge itself was nothing new. After finishing the book, I realised that Kazuo Ishiguro had used the exact same technique to tell the audience what would happen; there's never a Reveal, he just gradually allows us to guess, through scenes from Kathy's adult life, what's really happening. When it's finally spelled out for us, it doesn't come as a shock, despite how horrible it is. It's simply a confirmation of what we already pretty much knew - exactly as it was for the kids.
Religion Is Right: Literally right or not, does it really matter all that much? The belief Ruth and other clones cling onto, that true love will give you permission to live for a few more years, is technically secular in nature. But it also fill two other functions. One as a cry to the creators, a plea for them to recognize that the clones do have some inherent value, not merely a instrumental value as spare parts. Second, as a matter of how Ruth rewrite the story of her life, allowing herself to die with at least a shed of dignity. By choosing to believe in the myth and choosing to give up her potential spot with Tommy for Kathy, she gets to die as a martyr rather then a mere animal being taken to the slaughter. So while she failed to save herself or anyone else from death, she at least managed to save them from the dehumanization. Real Life religion can do the same thing, no matter whether the religion is technically true or not.
Religion Is Evil: For a story that is so much about the soul and the sanctity of the human life, it appears odd at first that religion isn't even mentioned once. It is mentioned that the clones are considered to have no souls, and that this have been proven untrue but nobody cares. So, how is the idea that clones have no souls justified in the first place. There's really only one option: The dogma of the "pro-life" movement, arbitrarily claiming that the soul is inserted in the body at the "moment of conception". Clones does not have such a moment, thus no soul. This setup may or may not be true for the book version as well.
Fridge Logic #1: Why go to the trouble of raising a human child to be perfectly healthy, educating them, and letting them loose on the world only to serve as spare parts later? It's harder to raise a child to adulthood than it is to retrain a new, healthy adult to do the tasks of an unhealthy dying one, and it's not like they're experiencing a population shortage to need to keep their existing population healthy.
Rule of Symbolism: The story runs on a psychologigal level - is is not meant to be realistic on a socioeconomic level.
Also, Hailsham seems to have been much more resource intensive than the typical facilities clones were raised in. When the protagonists found out about its history it turned out to be a kind of pie-in-the-sky project founded by idealists that folded pretty quickly. The institutions an average clone were brought up in were probably much more negligent. Also, I think there were some subtle indications that the economy WAS messed up. There wasn't societal collapse anything, but there were too many things/places that were run down or abandoned. Maybe the cloning project actually was bankrupting the government. If the promise of a cure to all disease makes the public so morally irrational, it's no surprise if they're being economically irrational too.
Fridge Logic #2: Why don't the clones just..run away? As far as I can tell from the film they aren't in any form of maximum security. People aren't keeping an eye on them much, they're free to travel wherever, and there's this vague understanding that they'll just willing to go to their surgery. They know what's happening to them, it's not like they have absolutely no idea, and they're old enough to not be completely naive, even if they were raised in a sheltered manner. Sure, the wrist monitors seem to track them somehow, but if worse came to it, couldn't they chop that hand off? If people can escape from soviet gulags, concentration camps, Alcatraz, surely the clones can go incognito or escape England at least? There's barely anything stopping them from just not going to their surgery.
Run away from their own identities and the purpose in life that they was created for? Over the millennia, there have been lots of martyrs who would chose death over turning their backs on what they believe to be their creator. These clones are like human, but they was created by the regular humans. Congratulations, clones: Your creators exist. Too bad they are cold and uncaring and totally unworthy of your loyalty.
In other words, they was conditioned to hate themselves and believe in the system oppressing them. They never managed to break free from this conditioning. Again, it's almost eerie how this story does not bring up religion at all. I mean, compare the slavery in the USA. The white slave-owners was Christian, so their slaves turned Christian as well.. starting preaching about how Moses fought against slavery! So, my question really isn't why they didn't run. Instead, it's why they didn't turn to philosophy or religion. They need to escape in their own heads before they can escape in the outside world.
It's probably an intentional wallbanger, designed to frustrate and enrage the audience. It's the oposite of anvilicious, really... If they had started running or preaching, the plot would have been reduced to "will they win or lose"... Much easier to digest, and also far less interesting in the long run. It would have made the story so much easier to shrug off afterwards...
They've been conditioned from birth to do as instructed and accept their fate. At Hailsham, they were fed the information without being explicitly told (as Miss Lucy says) so they would acclimatise themselves to their fate slowly enough that when it finally hits them, it's like something they've known all along and will accept. Also, escape is feared; that's what the stories at Hailsham about escaped children getting killed is about. It's explicitly manifested in their adult lives when Ruth refuses to go through a locked gate on the path down to the beach. They don't run because they associate the notion of escaping with death and suffering.