I see your point but it has to be more than that. These protestors must see that it's better to share these stops than to have extra cars on the street, or more crowding on the already shitty public transit.
In previous stories it was mentioned that the private bus would in some cases stop at the public stop and prevent regular public transit buses from using it for some period of time, forcing people to board the public bus not at the proper position and so forth.
Sharing a system of public bus stations requires some coordination, which it seems is just starting now.
The sentiment is that they are taking away housing options from people who have lived in SF for years and not only contributing to the gentrification of the community, but not even giving back or participating in it as well.
That comes back to the idea that people have the right to live where they like.
People who oppose gentrification believe that the government (or the "community") should try to influence who lives where. While it's absolutely true that people impose externalities on one another, this doesn't give the government carte-blanche to determine how people live their lives, or who should live where.
In the case of SF, the reasons range from the plausible (people of differing income levels living together contributes to the overall wellbeing of the city) to the discriminatory (artists are more valuable to the city's social life than tech works) to the downright nasty (tech nerds are bratty privileged rich kids)
And those people that complain are probably google users. I say fuck em! Google owes SF nothing, people live there by their own choosing, not because of anything google did, but just that SF is a great place to live (no polar vortex for one!) As for Oakland, I can only imagine that the injection of wealth by google employes spending some of their income in the east bay would be a good thing, it sure needs it.