I'm not going to tell you how to feel about the questions you were asked - you have the right to feel however you want to feel. However I would like to give you some things to think about, just so that you know for certain you aren't mistakenly throwing away a perfectly good job opportunity.
You say in your answer that "Germans can be quite direct". So first of all, you accept that there is a cultural difference and that the interviewer may not think or speak the way an American (like you) would in the same situation. There may also be a language issue if he is speaking English as a second language or you are receiving German as a second. Are you really allowing for that difference? If you don't think any allowance should be made then a second question to ask yourself would be isn't saying that all Germans are "quite direct" just as much of generalisation based upon race as the interviewer assuming that your family may have non-American roots?
Something that may be worth considering as a possibility is that the interviewer did not have your visa information. Even if you put it on your application form. I have conducted interviews in the UK (currently also in Europe!) and some large employers, notably government organisations, have a recruitment process that attempts to address prejudice or favouritism whereby the human resource department strip all age/gender/nationality information from applications before the recruiting managers handle it. Now, if there is a possibility that the interviewer did not know anything about your nationality as stated on your application would you still consider any question about your nationality to be "irrelevant"?
Also, crucially, you say that he is now waiting for you to confirm your interest. Does this not sound positive? If he really was a "racist", would you still be in the running for this job?
Rather than me tell you specifically how to express your disgust at these questions during your interview, I am just going to simply validate your feelings by saying that I understand why you may feel this way, and tell you that if you want to express these feelings you are at liberty to do so. Nobody should have to deal with racism, and I am definitely not telling you to put up with it - but properly consider it again in context before you go down the route of expressing your disgust because it will almost certainly cost you the job no matter whether you are wrong or right about the interviewer. Technically, there are precedents for calling out racism at job interviews that could see impaired decisions overturned - but this is very, very hard to prove, especially when there is doubt (and if I'm wrong about any of the points I've raised, you have to admit it is still reasons for doubt). You have far, far more rights as an employee, and employers know this so why would anybody racist employ someone who could call them out as such?