I might be wrong but if MN would extend the service to say Millerton and to Tivoli and make it just rush hour service and perhaps one mid-day train, I don't think people would mind it so much but to run bi-hourly service to these areas would kill the rural atmosphere of these areas. It would bring an almost subway-like quality to the service.
I don't think the issue is the trains (maybe it is for Millerton) but the rest of the stuff that goes along with having trains in the area. Yards (land use issues, lights, diesel exhaust, noise from idling trains, other machinery in the yards (e.g. Car Wash), parking areas for crew quarters, etc.)
The other issue is the biproduct of having commuter train service in your village or town - the inevitable desire to sell land to commuters. This can lead to subdivisions of existing plots of land, which increases the population of the area. Increasing the population will have additional effects on the infrastructure in the area (trash removal, schools, police and fire services, roads, etc.). One argument would be that the additional property tax revenue from the subdivided areas would cover this, but this is almost never the case, even if the relative property tax rates are equal between the "old" and "new" properties in the are.
When I was young I used to think it was very simple. Build some platforms along the ROW, add a parking lot and TVM, maybe a passenger footbridge or underpass to cross the ROW, and BAM! (like Emeril says) you have a train station. My biggest concern would be any signalling and track improvements you would have to make if the service continued beyond the station.
Now that I am older, and I have a better understanding of how government works (at least in New York), I know that it could never be that simple. A community can and probably will continue to feel the effects of a new station for a long time after service starts (some communities on LI are still tinkering with traffic light patterns at stations decades later)
I would love to see MN extend service as far north as they can, opening service up to as many communities as they can. But I also respect the wishes of communites along line, for they are fearful of what the long-term effects of commuter rail service will be on their communites.
One of the arguments that the folks in Northern Dutchess raised dealt with the degradation of service that would come if MN took over operations at Rhinecliff, since they assumed (and I think there is some truth to this) that Amtrak would probably look to reduce or eliminate service at the station. MN trains are slower and do not provide space (such as what is found in the club car) for riders to work while they are en route to NYC. Nor do they have provisions for power outlets that a person could use for a computer while on the train (while I think the coaches do have outlets, I don't think they are designed for passenger use, and I question how reliable the current coming out of the outlet is).
They also seemed to take issue (and this one I heard, not read) with MN servicing GCT rather than NYP, which also disrupts the "pattern" of the riders who commute from this area now (some people can no longer walk to their offices, different subways to use, etc). While it is nothing that is insurmountable, it is something to consider.
Maybe if MN planned on offering service to Penn Station (something the MTA considered) along with raising the speed of the service (I don't have all the performance specs of the Genesis engines so I don't know if this is possible) the communities in Northen Dutchess would not have *as much* to fear if the service was replaced by MN.