The founding father's used capitalization to put emphasis on certain terms. It seems to me that they wanted the well regulated Militia, made up of the people, to keep and bear Arms to protect the State and by extension themselves from a tyrannical federal government. If they intended the people to bear arms, why did they add the terms Militia, State, and Arms with emphasis but the people without it?
The only other place in the Constitution that speaks about what constitutes a militia is the fifth amendment, and it specifically only protects a Militia when it is in service to the government, which again is capitalized because they wanted emphasis that it was a proper militia and not a make shift one.
I agree with you, but I wouldn't read that much into their writing. The English language was even more lawless in their day.
In fact, the German-style capitalization of nouns may have just been a stylistic choice by the calligrapher:
Modern printings of the Constitution that follow the engrossed copy of the original can be identified by the many stylistic features in which Jacob Shallus's calligraphy departs from the style of the printers of 1787. The most conspicuous difference is Shallus's capitalization of almost all the nouns, in contrast to the very limited presence of capital letters in the work of the printers. The capital letters now help to give quotations from the Constitution, when taken from modern prints that follow the engrossed copy, an air of authenticity.