I question the author's fact-checking abilities when the article starts with the statement "the city officially gave the shuttles free rein to use public bus stops". Actually, the shuttles can only use 200 out of 2500+ muni stops and have a plethora of other restrictions. That doesn't seem like "free rein" to me.
See https://www.sfmta.com/projects-planning/projects/commuter-sh... for full program details, and http://www.nbcbayarea.com/news/local/San-Francisco-Muni-Appr... for a reference on the "200 out of 2500" statistic.