Back then the term militia meant any able-bodied male adult citizen. It seems to me that the Founding Fathers had two types of militia in mind.
From Article I, Section 8:
The Congress shall have Power:
Clause 10: To define and punish Piracies and Felonies committed on the high Seas, and Offences against the Law of Nations;
Clause 11: To declare War, grant Letters of Marque and Reprisal, and make Rules concerning Captures on Land and Water;
Clause 12: To raise and support Armies, but no Appropriation of Money to that Use shall be for a longer Term than two Years;
Clause 13: To provide and maintain a Navy;
Clause 14: To make Rules for the Government and Regulation of the land and naval Forces;
Clause 15: To provide for calling forth the Militia to execute the Laws of the Union, suppress Insurrections and repel Invasions;
Clause 16: To provide for organizing, arming, and disciplining, the Militia, and for governing such Part of them as may be employed in the Service of the United States, reserving to the States respectively, the Appointment of the Officers, and the Authority of training the Militia according to the discipline prescribed by Congress;
Later, in Article II, Section 2, Clause 1:
The President shall be Commander in Chief of the Army and Navy of the United States, and of the Militia of the several States, when called into the actual Service of the United States;
The above clearly define a militia organized for the defense of the nation.
Now, on to the famous 2nd Amendment:
A well regulated militia, being necessary to the security of a free state, the right of the people to keep and bear arms, shall not be infringed.
Now, the militia composed for national defense was clearly defined in the original constitution. The first 10 amendments (the "Bill of Rights") were ratified soon after to define the rights of individuals against the power of the government. It seems clear to me that the militia referred to in the 2nd Amendment was a People's militia, there to protect against abuses by the government, as is every other amendment in the Bill of Rights. This is the only logical conclusion, IMHO, given it's context in the Constitution.
If you disagree, and think this amendment refers to the army/national guard, then what is it doing in the Bill of Rights? Especially when national defense had been thouroughly covered in the original Constitution.