The right of the PEOPLE. Not the government (which is where the well regulated militia comes from).
The second amendment deals with two things. It says that the government is ALLOWED to create a well regulated militia in order to keep the country safe from foreign enemies (in our case, Al-Qaeda) and to keep citizens safe from other citizens (murderers, rioters, rapists, etc.)
And then it deals with the right of the PEOPLE to bear arms. It says that the government CAN NOT infringe on this right. This is why the comma was conveniently placed. This itself is for two reasons:
1. For citizens to protect themselves when the government can not.
2. For citizens to be able to fight back when the government has become tyrannical.
The right to bear arms is not practiced in tyrannical governments for a reason. It's hard to uprise when you can't even fight. This is why Cubans have been escaping to America instead of fighting the regime. They have nothing to fight with.