They did business with German companies, of which there were thousands of other companies that did the same thing. The relationship started in 1926, Hitler didn't come to power until 1933.
I don't know why people find it necessary to defend the old timers that made their families rich long ago. Guys like Prescott Bush and Joe Kennedy appear to have been involved in some shady deals and practices that brought enormous wealth to their families. The legacy of that kind of thing is that we end up with leaders who got to be leaders in large part through inheritance and connections rather than true and genuine worthiness and a self earned position acquired through merit. It has no reflection on the goodness or character or worth of the person in question. They can be very fine people, but they got their wealth, station and position in life from being born into specific families and circumstances.
No matter how you spin it, Prescott Bush had bank assets seized under the Trading with the Enemy Act in 1942. That means his bank was doing business with Nazi Germany while it built the German war machine and was invading countries of Europe and rounding up Jews and others for it's death camps and forced labor camps.
George Bush had nothing to do with it. He wasn't even born. Prescott's son, George H. W., almost lost his life fighting in the war he in an indirect way helped to create. No matter how you cut it however, the family wealth at least in part, comes from those disreputable shady dealings.