Funny? How do you figure that?
I think that it would be disgraceful honestly but then again, I am an American that has lived here in Germany and seen what it has done to this country and everyone else around it. No, I personally wouldn't find that funny at all.
There are other flags for Germany but I think that the current one would be cool.
As for putting the a flag on the roof, it can be from any country. The idea of doing that is giving your mini a personal touch and that is one way of doing it.