A Shays' Rebellion question! My favorite!

The primary weakness of the existing governmental structure that the rebellion exposed was the inability for the Massachusetts Governor to quickly raise the troops necessary to fight off the rebels.

You mention that the rebels were fairly easily dispersed once a formidable fighting force was created to opposed them. However, what you're missing is how long it took and the difficulty in creating that force.

Governor Bowdoin attempted to raise the state's militia after the rebels had begun shutting down courthouses across the state in August/September of 1786, but because the militia was made up of the same kinds of people rebelling, the local units refused to act. I did a fair amount of work on a transcript of a trial in Worcester that took place after the rebellion. There were many leaders of the local militias who were tried for aiding the rebels or participating in the rebellion themselves.

It is also important to conceive of the rebels as less akin to a dumb "mob" and rather think of the event as the rise of an entire oppressed socio-economic class. The latest work on the rebellion tells the story of a deeply shattered economic structure for the Western Massachusetts farmers that was inflamed by a strong power base in Boston. We have a merchant class in charge, and they were simply unwilling to govern for their whole state. This is the framework we should be using the understand the local militias and their reluctance to take up arms against their neighbors.

After his own militia failed to act, Governor Bowdoin asked his neighboring states to help by using their militias, but he received no such help. So, lacking a federal army to ask for assistance (remember, we're still in the Articles of Confederation here), Bowdoin has to use the Bostonian merchant's deep pockets to cull together a last-minute force of mercenaries. This group is by General Benjamin Lincoln and eventually marches out in late January 1787. The rebellion is dispersed in early February.

Rebels are shutting down courts in August, and it's only until the following year that the state government is able to pull together a force to fight them.

The reason this reverberated across the nation was a result of this inability for Massachusetts to quickly put an end to the problem themselves (although they eventually did). The concern was that this kind of action could happen in any of the states, and the powerlessness of the states in the face of such an uprising was a troubling thought. The rebels got very close to raiding the federal arsenal in Springfield and had a control over much of the state's courthouses, effectively preventing the state government from functioning in the western 2/3 of the state.

Federalists saw a strong, centralized national government as a way to prevent these kinds of flare ups in the future.

If you're interested in the macro-level economics of the time period and a even-keeled take on the rebellion, then David Szatmary's "Shays' Rebellion: The Making of an Agrarian Insurrection" is the seminal work on the real underlying issues of the day. If you are looking for more narratives and individually-based description, then Leo Richards's "Shays's Rebellion: The American Revolution's Final Battle" is for you.

This topic is definitely one of my specialities, so I'm happy to answer any other questions you might have or clarify anything I've written above.