The message is right on - the tension between security and comfort is as much a part of the war on terror as it is a part of the whole internet experience, or paying for goods, or just getting through your own front door. There comes a point where increasing security - to preserve your freedom - you actually relinquish your freedom, and you become worse than the threat you feared.
Little Brother takes the reader through that dilemma, in a well thought out way. Sadly the technology is complex, as are some of the concepts of security (both physical and cyber) and we end up with a few too many infodumps along the way.
The tension builds nicely through the book, but you do wonder how the protagonist is going to triumph over the villains, even with his greater understanding of cyberspace - and that's a good thing. A good novel should never look like a cakewalk for the protag. Unfortunately the poor protag falls into the villains' clutches a second time, and it really does look to be all over, until the cavalry ride over the hill. Then it's celebration and fireworks, yet somehow the villains escape justice, setting up for a sequel. It all happens a bit too quickly, and feels rushed, else I'd have happily given 5 stars. After all, I don't mind pat endings - they're what this genre is all about - it's just that I was disappointed that the ending was so patently "and they all lived happily ever after - until the next crisis". I did see the protag grow and change through the book, but in real life, there so often a price to pay, and the protag didn't pay it. The cost was entirely borne by the minor characters.