If anything, it says that if any arms ARE protected, it's those that the military uses, e.g. M-16s and M-60s. So when people cite Miller to support an AWB, they twist things oppositely to what was intended. (As usual.)
In a literal sense, I think you're exactly right. At the time, the Founding Fathers clearly desired that the citizens had some kind of military parity with the government. The term 'bear arms' has a deeply military connontation, not a hunting one.
Now, does that mean that Thomas Jefferson wanted individual citizens to own cruise missiles? Tanks? Grenade launchers? It's hard to say, exactly, since they weren't around at the time. Certainly private citizens owned ships and cannon, which were clearly military grade of the time. A letter of marque serves no purpose if there aren't heavily armed citizens to employ. One could infer that the Founding Fathers wanted the citizens to have pretty much anything that the government could.
At least in the late 18th century. How about the early 21st? A lot of the problems herin is that they never imagined we'd be operating on the same Constitution (amended or not) over 200 years later. It seems to me that under what appeared to be their intent, they'd be more open for the banning of handguns (as they are more useful in crime than in warfare) than for any restrictions on rifles, machine guns, or heavier items. Just my take, anyway.