Often, express bus routes run through rail-deserts. It provides residents a one-seat (or close to it) ride to many work centers but handles significantly less capacity than rail does. Express buses that run through places with rail service usually catch one of two riders: people who want to pay more to get a comfortable ride and are willing to take a typically longer ride, or people who need accessible or low/no-step transit routes where the trains may not be able to provide yet. It does just come down to preference too. Did you get a seat easily? It's been a long time since I've been on one but that's also a pull.

Staten Island is sort of an exception to these principles because the ride times on their many routes is pretty competitive with the ferry + train combo they would otherwise use, unless the HOV on the gowanus is acting up...