Being a doormat is not something readers generally find appealing in any character, and particularly in a main character. Give her things to do and let her do them. Let her take risks and sometimes succeed and sometimes fail. Let her pick a goal and commit to it and pursue it. Let her, as you say, make choices. Otherwise she isn't really a character; she's exposition with a face and a name.
Book middles frequently involve beloved characters being in serious peril or coming to harm, a proliferation of plot threads that can feel out of control, or a mess of problems with no apparent solution. These are things that can be genuinely hard for writers to face, just as they're hard for characters to face. It's so much easier and more enjoyable to focus on the beginning, when everything's fun and exciting, and the end, when all the questions are answered.