The Northeast trains go through some neighborhoods in the cities where "youths", as they call them, like to throw rocks at passing trains. It's a lot less of a problem now than it was in the 1970s, but it still happens. Reports of rock throwing were part of what happened with the NER 188 derailment back in 2015.IIRC the Amfleets were originally designed to feel like airliners and the small windows for some reason.
Anyway, if the windows are smaller, there's less of a chance that a rock will hit it.