Legitimacy is decided by the victor, just read the Declaration of Independence.
What is important to keep in mind when reading the bill of rights is that the framers didn't consider the constitution as a document bestowing rights on people. God (or nature, if you prefer) gave us most of our rights, and they listed just a few particulars that no legitimate government has any business messing with.
Every man has a right to self defense. If you attack a man, he will defend himself. Actually, if you attack an animal, the animal will defend itself too, since God granted that right to every living then, not just man. No law can prevent that, and no legislature should even try. As Europe is probably going to learn in the next few years, self defense includes defending your family, your nation and your country.
The framers most certainly did consider revolt to be a God-given right, one that they had just exercised. Defense of liberty was at least as important as defense of body, nation or country, and the 2nd was written to support them all.
Likewise, no law can change a man's thoughts, or his conscience, so we have the 1st, the 4th, the 5th and the 9th. (The 1st is actually more complex than this, because the "no law respecting an establishment of religion" they had in mind was about the colonies that had state religions and wanted to keep them...)
The 3rd, the 6th, the 7th, the 8th and the 10th aren't exactly rights, though they do use that word fairly often. They were abuses, the sorts of things they had just fought a long and bloody war to get away from. They were creating a new type of government, one that was below the people, not above it. Being below the people, it should not have the power to bully them. Since they lacked the authority to personally bully their countrymen, they refused to "delegate" that authority to their government.
Of the 10, only one of them survives today in a form that would be recognizable to the framers, and that is the 3rd, which is really sad.