It so varies. I've used my NEXUS to check in online and then to check a bag at the counter, only to be told at boarding that I'm required to show my passport. Agent at YYJ threatened to not let the SE ahead of me fly when he presented his NEXUS and argued that it was sufficient. I'd also planned to use my NEXUS, and my passport case had, of course, slipped to the bottom of my bag under my laptop, so it was a bit of a thing to dig it out.
Different airports, different days, different scenarios, different answers. Did have NEXUS accepted for check in and boarding at SFO recently, though. YMMV?