My main beef with signal is that they release their encryption libraries as GPLv3 not LGPLv3, preventing the use of them in any commercial product that doesn't want to open their source code.
Yet, they "worked with" Facebook and WhatsApp to incorporate their protocols presumably providing them with an alternative license. It sure would be nice if companies who wish to add encryption to their messaging products, but didn't have the pull of the bigger guys to warrant OWS's attention, could just use an LGPLed library to do so. If OWS's mission is to bring about widespread encrypted communications, playing favorites with a few larger messaging companies seems to send the wrong message.
(The points made in the article, while valid, seem to be splitting hairs relative to the overall net good Signal has provided.)