The homeless aren't scared of a bus driver. Nor are passengers - on some routes in the evenings people would jump on via the back doors and refuse to pay fare. The bus driver would refuse to move the bus until they came forward and paid the fare. The bus driver always lost.
The reason why these problems aren't endemic in NYC is because NYC has actual enforcement via the NYPD. The police is widespread and available enough that no one tries to fuck around with the system too hard. In Seattle the SPD never show up to these things unless violence erupts.
The NYPD also has, for better or worse, a traditionally less soft stance on vagrancy and fare jumping.
http://en.m.wikipedia.org/wiki/Broken_windows_theory#New_Yor...
As someone who grew up in a very liberal part of the west coast, it's hard to admit, but authoritarianism and ubiquitous police presence has done wonders for this city. It certainly unseats some assumptions.
The trouble with the success of broken windows in NYC though, is that it has created a culture where increasingly authoritarian policies are tolerated, and results proving their efficacy often not provided.
Bit more detail: http://blogcritics.org/policing-urban-crimes-the-broken-wind...
Even more on wikipedia: http://en.wikipedia.org/wiki/Broken_windows_theory#Criticism...
[1] http://www.huffingtonpost.com/2013/03/05/nyc-homelessness-ri...
In the context of NYC: as it is there is little stopping a homeless person from jumping a turnstile and spending all day or night on the 24 hour subway system. But it's fairly rare to see this (I believe it used to be much more common). I imagine on a bus, where there is always a city employee monitoring things, it would be even more rare.