Scientists have been writing down sets of rules to describe the workings of the universe for as long as there have been scientists. These rules help us extrapolate what will happen next in a given situation, and if those extrapolations turn out to be wrong, the scientists will run to their chalkboards and write down new rules until the whole system of rules conforms to what we know about reality.
So the universe would appear to be rule based; most people will agree to this (in its general form). But if it's true that everything in the universe is rule based, then it also means that people must be based on rules. This goes against what we feel to be true about ourselves. This gut feeling exists, I think, because it's too difficult to extrapolate both our thoughts and our actions. In part this is because the brain's "processing power" is taken up by thinking about the brain when we try to do this, and in part it's because our information about the brain is incomplete in even the best of circumstances (i.e. under an fMRI). Even the best techniques of today can't predict a person's actions at even the most rudimentary level.
If the universe is rule based, then the people that inhabit it must also be rule based, and strict adherence to the rules means that any choice is essentially fated to happen - or, if you buy into some interpretations of quantum mechanics, the "choice" is not under your control but instead the result of electron spin etc. Consciousness itself is an illusion.
Even if things like consciousness and free will are illusory, it doesn't mean that they aren't useful. Obviously the justice system would have to work very differently if people thought that things were not your fault because there is no real "you" to speak of. Our society is founded on the belief that some things matter and others don't, and without these constructs society requires remodeling (especially if morality is itself a construct).
One of the reasons that I don't like writing about philosophical issues is that I'm very aware that they've been rehashed a thousand times before, and that I'm unable to actually add anything to the global, scholarly conversation. I actually feel this way about a lot of things; there are a large number of people who are much smarter than I, and typing away at my computer serves only selfish purposes. But to examine our beliefs requires conversation, and since I have no one to really talk about these things with, it needs to go out to the internet instead.