Why do I stay in a relationship when I know it is not working?

FEAR. Plain and simple. You are afraid to be alone.  You think if you leave this person you may never find anyone else.  Also there are some qualities in this person  you don't want to do without.  It becomes second nature to overlook unhealthy behavior.  For instance if there is emotional abuse it maybe down played because there is no physical abuse. There will be a point when you say enough.  I hold the space for the best possible outcome for your life.