On balance, a computer-controlled personal transit system is likely to tilt the balance towards the authorities. The getaway car from a robbery goes directly to jail; it does not pass GO or collect $200. Surveillance can be automatic and frighteningly effective; see SecurityAndPrivacy. Also, any desired number of police can be deployed rapidly wherever they are needed. (Much more)
Skytran should have strict policies on record keeping and purge the history on point-to-point travel on a rolling weekly basis. If a crime has been committed usually it is known fairly quickly and a warrant could be issued for targeted information, such as where a mugger traveled to after accosting someone on a station. It should not be possible for the government to capture point-to-point transaction data to cast a wide net over it's citizens.
Keeping the pods clean will be an important part of the system.