Ingress, since the beginning, has been a very player driven game. Portals, aside from an initial set of libraries, fire stations, and other public landmarks, are submitted by users. When Niantic decided to reduce the mod slots available to a player per Portal to one, the players piped up and got it raised to two (not a huge victory in my opinion). But boycotts on new game mechanics, such as the Jarvis Shard boycott in New York, can be caused by players as well.
If you have taken a look at the Jarvis Shard contest, you realize it will take a tremendous amount of cooperation between cities and regions to move the shards to your factions goal. From reading about the Jarvis Shard in New York, it sounds like the Resistance there had come up with plan to successfully move Shard #1 for their faction. The plan was to move the Shard to an island, where it could be held and await a clear path out of the city.
Once the Shard had been move to the remote island, a complaint from a user resulted in the Shard being moved by Niantic to a Portal it had never been to. In other words, it was moved not by the mechanics set by the rules of the game, but intentionally to a more accessible area. This move was a major misstep by Niantic and is indicative of problems that Ingress will face as the game comes out of beta.
If Niantic makes snap decisions based on a few Agent's complaints they are going to have a huge problem as the number of Agents grows. It is already evident in the Portal reporting process, a single Agent seems to be able to report a problem with a Portal and have it removed. In my local area, this has resulted in the trimming of Portals maliciously by the opposite faction from our strongest areas.
Niantic needs to be more cautious, not making mistakes like moving the Jarvis Shard and tampering with game play again. Operations, like the one the New York Resistance pulled off, take a tremendous amount of commitment and time. Simply killing that effort in response to a single Agent complaint is deflating and a boycott is understandable. I would encourage the Agents involved to continue the fight though, Niantic has heard your complaint and I hope they will make changes to ensure this doesn't happen again.
You can find the New York Resistance Boycott post on Google Plus, the Agents involved have signed the letter in the comments. Since the post went active, Jarvis Shard #1 has moved to Florida and at the time of writing this the Portal is in Resistance hands.