For me, the worst treated companion has to be Nyssa, purely because of how inconcievably calm she is around The Master during her various confrontations with him.
Let's think through what the Master did to Nyssa. First he possessed and killed her stepmother AND her father, then took the form of her dead father and tricked Nyssa into helping him with a plot which destroyed quite a lot of the unverse, including Nyssa's entire planet. And just to top it off, he killed the Fourth Doctor as well... and got away with all of this scot-free.
If I was Nyssa, by the time of Castrovalva (where she kidnaps and in her mind, possibly kills Adric) I would probably have gone beyond dirty looks...