Regret having Sex with him

I've been with my boyfriend for two years and we've been having sex during most of it. During foreplay, I honestly do want to have sex with him, but when he goes to put it in, I start to question whether or not I actually do, but I go along with it. The sex is good and I like it, but afterwards I regret it. Before getting into a relationship with my boyfriend I was raped over the course of a few years. And my boyfriend has helped me a lot through that, but does this happen to anyone else? I don't know how to explain it to him because I honestly don't know why I regret it. Any advice?