According to James Madison, less than 20% of the population. Not everyone. Not even close.
We can see by the description you provided that it was limited to able-bodied, white, male citizens, 18-45 years of age.
Their RKBA was protected by the second amendment.
Er... no. As has been pointed out, that it only a limit on who may serve in the active militia. There is no such limitation in the text of the Second Amendment itself.
That each and every free able-bodied white male citizen of the respective States,
For lack of a better word this is the "pool" to be chosen from. Now granted slavery existed at that time but that has been addressed along with womens rights.
Also note the individual called for service was to supply his own arms. If one didn't already have said weapons there were to be acquired by that individual. Not given to him by the state of federal govt.