I would say there are two main sources of shock in these cases: the physical violence and the psychologic violence.
I don't think there is much to say in order to explain why the physical violence is shocking. That's the most natural thing, which we can observe in animals' behavior too. Living rational creatures are afraid of what hurts them, which is a defensive system. Fire hurts you, you're scared to fall into it so you won't jump into, which will keep you from accidentally killing yourself. So being assaulted like that by a being of your own species, that you normally would not be scared of, basically fucks with your mind and causes a trauma.
As for the psychologic violence, the way people feel ashamed or dirty (etc.) because of the sexual act performed against their will, that is something "unnatural". Please don't judge me too fast for these words and let me explain what I mean. In the wild, there is no such thing as rape. You'll see everyday dogs copulating with the first female they see, the female will try to keep him away half a second but once the action is over, it does not feel dirty or shocked or anything, it just keeps going with its life. I think social codes are what creates this psychologic trauma about that forced sexual act. We have been taught to respect our body, to keep it from being seen and touched, to keep it only for a few "chosen ones". We have been taught that we have a right of privacy and use of our body that no one is allowed to take from us. Sexuality is still quite a taboo, showing one's sexual parts in public is strictly judged as shocking and inappropriate by the great majority of our society so seeing our most intimate privacy being violated with such brutality suddenly hits all these codes that we have learnt to the extent of taking them for granted in our values and thoughts. I think that's why, or I least that's one of the reasons why being raped causes such trauma.
Of course, by calling it "unnatural" I am not saying that is a social code we should stop creating in order to get back to a more "natural" way of seeing things. I am not AT ALL trying to say a rape is not a big deal and I am not AT ALL trying to say we should stop thinking of it as such.
These topics, and questions such as these, are often polemical, controversial, and I know some people here have experienced (or know people who have experienced) horrible things and might get uncomfortable, shocked, or offended by what I said. It is a topic charged with a lot of emotions and before getting any mean or virulent reproach for what I tried to say, I would argue that I am just trying to find a rationnal answer to the question asked above. If anyone does not agree with what I said, I am ok with talking about it, comparing ideas, and being proved wrong as long as there can be an actual discussion. Once again, I am conscious this is a huge emotional load for many people and in under no circumstance have I wanted to offend anyone by trying to rationnal something that is socially considered as a horrible and cruel thing, which I also think it is.