Of course, there are legitimate issues and concerns, such as noise, construction impacts, and whether private properties are needed for the train right of way. Unfortunately there's no answer to many of these questions. Remember, this is just the beginning of the design and engineering process. Also adding to the uncertainty, the High Speed Rail Authority has yet to hammer out an agreement with Caltrain to share the corridor.
However, some of the comments raised by NIMBYs are simply outlandish:
"We just had a stupid meeting in San Jose discussing this BS train which they intend to run through every quaint peninsula town- that would be starting with WILLOW GLEN in San Jose, through Santa Clara quaint downtown, Sunnyvale, Mountain View (nice downtown there), Palo Alto, Atherton where this POS train goes through Larry Ellison's BACKYARD, Menlo Park, Burlingame downtown where this POS will ruin every 4 star restaurant there and up to SF.And more...
"If they don't build this crap project UNDERGROUND this project will be sued repeatedly until all hell breaks loose by the richest people in the country. What a bunch of losers."
"I hope that with this news, some avid HSR enthusiasts begin to grow a conscience and see that air travel between SF and LA has very very little to do with the Peninsula, and HSR trains may be a reduction in air emissions, but will be a huge net increase to carbon emissions in the Peninsula - because of the auto traffic that will be drawn directly and deeply into Peninsula towns which do not host major airports."
After filtering these comments, the only consistency you'll find is that they don't know much about HSR, that HSR is not good only in where they live, and that HSR ought to be invisible. Also, many of those who commented tend to come from wealthy neighborhoods, and therefore have a stronger sense of entitlement.
Is their fear substantiated? You don't have to travel across the ocean to see that isn't. For instance, there's a 4 track electrified railroad passing through the suburbs of Philadelphia. As you can see, many of these stations have a stronger small-town, suburban-feel than those on the Peninsula.
In addition, there's a false perception that putting the trains underground will solve all problems. The reality is that not only putting trains underground increases construction costs multiple times, it tend to cause more construction impacts onto the community (imagine lines of concrete trucks coming in). With underground construction, the crews would sometimes accidentally cut off electrical or water lines, or cause adjacent buildings to subside.
The dialogue between the community and the High Speed Rail Authority is important, so is the education about high speed rail. Realistically, system requirements would be better defined and somewhat scaled down (value engineering) to reduce cost over time.