They're used in some subways - boston & new york at least - though I don't know if these are just trials or if they've perhaps ended. You definitely can't walk into a merchant and expect a contactless payment though - I'm pretty sure merchant roll outs so far have been limited to pay at the pump trials.
Although it also doesn't cover the entire system. The commuter rail trains go out where they can't rely on wireless coverage (in fact, there's at least one stretch on my line where we can rely on not getting coverage), so they can't install the card readers. As a result, the monthly passes for zones beyond Boston are still in ticket form.