O man... I have been in this situation. My wife initially didn't want anything to do with sex. Everything was gross or bad. This went on for years maybe even a decade. I cared about her and wanted to help. Over the years I thought it was trauma, she was gay, I wasn't attractive enough, blamed my abilities (though I had never had problems with other women). It was very stressful on both of us and almost ended my relationship multiple times. In the end, you are right it was just time. It is like a sexual young girl. She was a Virgin when we met and it was really because her sexual being had never been formed. Here are the suggestions I have:
Start off slow outside of the bedroom. Try to find things that turn her on. Movies, talk more about sex. The trick is to make her horny without it being in a sexual situation. She may try to change the subject. She is not use to being turned on and it is a bit scary (for lack of a better word). Sit her down in the kitchen and explain how important sex is and describe how it makes you feel and how you want it to make her feel. You want it to be a good loving experience for everyone.
Don't put to much pressure on the actual acts. Just make her sit through a moderately sexual movie (don't start with 50 shades of grey or anything). It is all about overcoming the idea that sex is wrong and bad. Point out articles from r/sex with ideas (very calm ones) in places were you cannot actually do them. Show her this article (look this sounds like us). Even if she understands that sex is natural and good at a academic level she still hasn't understood it subconscious level. Take time to get her there. I suggest even possibly forgoing attempting sex for a while and focus on developing her arousal outside of the bedroom. She may be more receptive than in the bedroom where she already feels there are expectations she cannot meet.
The next step I would do is to go back to middle school. Try making out on the couch or dry humping. Clothes on activities and then stop like your parents came home. Do not move it into the bedroom until she wants it. I know this all sounds crazy.. but it did work for me and now my relationship is in a really good place. I just stay on here to try and help people get through it.