Misandry is ideological, which means its mostly a choice. A phobia is reflexive, its maladaptive and beyond simply choosing because illogical things can't be logicked out of.

Its like the difference between hating blacks because you took a look at economics and crime stats or hating them because you got mugged by one and now have anxiety attacks when you see them. The end result might be similar, but otherwise its a huge difference.

Both words have their use in dealing with two different types of people and why they are the way they are.