Where do you get the idea that the towns around Manchester and Nashua are all just a few thousand people? It's entirely--and as I'm beginning to expect, unsurprisingly--inaccurate. The first four cities in towns along the Capitol Corridor in New Hampshire are Nashua, Merrimack, Bedford and Manchester. Bedford is the smallest such community at a little over 21,000. Even without the leadership of Manchester's mayor (which I consider shameful), the town and city councils of all those communities favor rail, so I'm not sure where you get the idea that "these small places are not going to be interested".
And despite what some people like to think, New Hampshire is not a "home rule" locally-based state, but a Dillon rule state. The state, not the towns, has the authority to determine transportation infrastructure and planning. I'm not really sure what your point about the emphasis on towns is, but it's beside the point anyway, since (again) the overwhelming majority of residents from every area (and political party) in the state supports the Capitol Corridor, as do the local governments of all the towns along its proposed route.
While I would also bet that most people traveling I-93 and Route 3 are headed to places other than Boston, your anecdotal arguments don't cut it. Despite what the Executive Council seems to suggest, a properly functioning state relies on facts, not anecdotes and preconceived notions for its policy making and planning. And as the Boston Express buses on I-93 and Route 3 show, there are plenty of people commuting from the area directly to Boston. If they're willing to sit in traffic on a bus for $18, I bet many more people would be willing to get to their destination faster and in more comfort for something closer to the $7.25 that it takes to get from Providence to Boston on commuter rail.
Commuter rail, despite its name, is not just for commuters. I don't think many people commute from Providence, but people from Providence or Boston can take a train to visit the other city, whether for work or leisure. It makes Providence a more desirable place to live due to its modern, convenient connection to Boston, and it makes it easier for businesses to attract workers. The same would be true of Manchester and Nashua.
Your argument also ignores the new development that rail would bring. Train stations in downtown Manchester, Nashua and Concord would almost certainly be surrounded by transit-oriented development. Even Bedford has expressed a desire to explore TOD around the airport station. Rail would serve the new residents and businesses around these stations, as well as current residents who could hop on the train from Manchester to get dinner in Nashua, or from Nashua to a show or baseball game in Manchester without worrying about parking and traffic.
Unlike highways, rail is not just about transportation infrastructure, but also the livability of cities and denser suburbs. New Hampshire is losing young people, who are looking for more dynamic cities, and Manchester loses young people even in-state to Portsmouth. Having a quick, easy connection to Boston and the development it will help spur in downtown Manchester will make the city more attractive to young people and families looking for a smaller, but still urban alternative to Boston and Providence.
It's clear, though, that you either have an ideological opposition to commuter rail, or that in the absence of facts you have become entrenched in your opposition. You keep changing the criteria--first the area has to be urban, but when it proves to be by both your and the Census Bureau's definitions, now it has to contend with New Hampshire's mythical (but incorrect) local control. You clearly don't have a very strong knowledge of either the development or political will of the people and municipalities in the Merrimack Valley. It is a generally concentrated, and in Manchester and Nashua rather densely built area, in which 75% of the people want a commuter rail connection to Boston. That's not an anecdote--those are facts from the UNH poll and the Census Bureau, which by the way
does make some adjustments to its urban criteria based on the specifics of the region.
But again, the real issue here isn't even the commuter rail, itself, but the study that would have provided the facts about economic benefits and costs. You have yet to offer any reason to oppose that study. But I suspect it probably stems from the same reason that Colin Van Ostern, who is running against Executive Councilor Dan St. Hilaire this fall,
surmises in yesterday's Concord Monitor for the opposition of Councilors Wheeler, St. Hilaire and Sununu: