"I cant imagine hes intentionally trying to upset me so I feel guilty telling him that I feel upset."
This is the problem, right here. You need to wise up, and fast. You need to be able to understand that, actually he is intentionally trying to upset you. But he will never admit to that, no matter what you say to him.
Abusive men (such as the one you are with) seek out women such as yourself (and such I used to be) who can't imagine how unspeakably awful one human being can be to another.
The fact is, you were recently raped, and he is deliberately making jokes about it. And when you asked him not to, he got angry with you. You can't understand why anyone would do this, so instead of seeing what is right in front of your face - a total piece of shit - you were looking for other reasons to understand "why" he would say it, and you are internalising the bad feeling (e.g. feeling guilty for bringing it up) instead of putting the responsibility where it lies - with the utter lowlife who is enjoying making rape jokes to a rape victim.
You should be proud of yourself for starting this thread, it is your voice of reason questioning his fog. And if you stay with this man, he will surround you with fog and get you doubting your own feelings - because he treats you nicely on the surface, he couldn't mean it could he? Yes he could and he does. This man takes pleasure in making fun out of you.
Run, please. It took me years to understand the simple truth. There are some fucked up people in the world, and some of them mean you harm. Even sometimes ones who say nice things to you and make you feel wanted. Look at what's actually going on not what he says. And please don't whatever you do fall into the trap of trying to get him to admit what he's done, or understand how you feel. It'd be a monumental waste of time. Anyway, he probably can't properly understand how you feel, just as you don't really understand how anyone can be so cruel. In normal relationships, if you decide it's just not workingm you owe the other person an explanation. If the other person is abusive or manipulative, you don't owe them anything, no sit-down-chat or whatever you would do with someone who deserves respect.
Someone who jokes about rape to a rape victim doesn't deserve their feelings taken into consideration in any way.
Just do what you need to to get away.