You can set up an illegal radio station for less than $1,000. My friends and I did so in Virginia, in the USA, back in 2002. We were out in a rural area of Virginia. We had great fun playing our favorite music to whoever would get the signal. The FEC is slow to crack down on stuff like that when you are out in the middle of nowhere. The radio station lasted 2 years, and it only got shut down when we moved on to other things. I have fond memories of it.
Running a radio show is great fun and, if you are an extrovert, it can be addicting. So why don't more people do it? Because it is illegal.
Likewise, if you created a protocol so free that government regulation was impossible, then the government could simply make it illegal. You would be "free" to use it, just like I was "free" to setup an illegal radio station, but most people won't go near it if it is illegal.
There are many things that go through our society, and which flow so freely that the government doesn't have the power to stop it, so instead it increases the penalties. Drugs would be an example. In that case, a lot of people get scared away from drugs simply because the government policies are draconian -- small amounts of drugs, found on your person, can lead to years of pain and legal trouble.
I agree with the other comment where someone says that you can not come up with a technology that will solve a policy problem. The ultimate power of the government is that, in the end, to uphold the legitimacy of the law it has the power to kill people. You can't come up with some cool technology that lets you get around the reality of a punishing government, if the government decides that some technology is too dangerous. All you can do is what the people of Syria are doing now -- organize, resist, protest, possibly even fight. There are only political solutions to political problems.