"Pusher has always worked across a wide variety of devices via a Flash based fallback mechanism, and we haven’t replaced this option in the newer version. Since the Flash version uses the WebSocket endpoint, it gets all the low latency, low overhead advantages of WebSockets. The drawbacks with this approach are that it involves downloading extra files, Flash isn’t installed on every browser, and certain ports need to be open on the client’s network."
The preference is always to get some sort of websocket connection. If native websockets aren't present and flash is enabled, it'll try to create a websocket connection via flash first. It's only if that fails for some reason that it tries to connect via other means.