I don't think they are saying that the typical user will experience a 5 minute longer delay; rather, the typical user will experience a shorter wait time. If the entire system is 40% more efficient, then even if you have to wait a little longer because the cab goes a little out of your way, that should be offset by a lower wait time. *Some* users will experience higher wait + travel times, but as they say here, no more than a few minutes.
The reason that they bring it up is because there are certain kinds of optimizations that will optimize the heck out of the average value, but they make the worst value an order of magnitude worse. For example, imagine a new proposal that would keep all the cabs in densely populated downtown and never go uptown whenever there was anybody waiting downtown. If there was a big enough ratio of people downtown versus uptown, then the average trip length would get better under this proposal, but the worst waiting time (for the uptowners) would be terrible.
Having said that, part of the reason why people take cabs is to get exactly where they are going, as fast as they can. If they wanted to get approximately where they wanted to go, with more people onboard, they would take a subway (or even the bus).