The right to safe transit
In an earlier comment thread, Cavan reminds me that some people can justifiably feel uncomfortable on transit because of raucous people, inappropriate behavior, etc.
While I don't think that justifies creating separate shuttle bus systems, I do think we need to address the problems better than we do.
For example, I was on a subway car not quite two years ago on the red line between Union Station and Brookland and there was no question things were out of control.
With regard to harassment on transit, the New York City group New Yorkers for Safe Transit is one that focuses on this issue, and the group was mentioned in this NYT article, "New York City Officials Look at Subway Sex Offenses."
Prof. Anastasia Loukaitou-Sideris of UCLA has studied this issue as well. Her work in this arena is covered in this U of California online article "Women and Transit: Making Bus Stops Closer to What Women Want."
While the article covers research on bus stop safety, it discusses an important finding of the study, that the reason that perceptions of crime aren't reflected in actual crimes according to the statistics, the reality is that many of the problems and even crimes, such as inappropriate touching and utterances, aren't reported.
I'm sure this is true of being on the bus as well.
Also see "What Women Want: Transportation Research Expands in Scope and Relevance by Pursuing Questions Related to the "Other" Sex."