The founders may (or may not) have envisioned an armed populace as a means of thwarting the raise of a dictatorship. However, they could never have foreseen the technological arms development that has gone on since that time. The weapons available to citizens can no longer stand up to modern militaries.
The Whiskey Rebellion is a good historical snapshot. The fledgling US government wanted to raise money by taxing whiskey and other spirits, and the people didn't like it. George Washington sent in troops to quell the rebellion. So right away in the US we have the very situation you are describing. In the end, Washington was able to quell the rebellion and an armed populace didn't stop him from doing so.