It sounds like your boss isn't a very good manager in some ways. Maybe she would be open to feedback if you talk to her about your frustrations. I can relate to what you are saying. I'm a graduate student too, and went back to school because I needed a professional career to feel like I was living my life and reaching my potential. It really is frustrating to be trying to establish yourself as a professional, and not to be treated like they even trust you with basic things like having a key or managing your own time. Part of it might have to do with being in school and that being the priority, as they might feel that they aren't your priority so that affects your status with the company.

Some companies are more supportive of increasing your education than others. I would suggest evaluating your needs and asking yourself if this company can meet your needs or not. You can present your needs to them and see if they will offer changes that will work for you. If they aren't meeting your needs, you might want to find someone else who will. It is reasonable to want a job that recognizes your capabilities and potential and helps you to feel good about yourself. Sometimes speaking up for yourself can make that more likely, and sometimes they aren't willing or able to give what you need. Maybe they need to be reminded of your potential and abilities so that they will recognize what you have to offer.