The Nazis eventually had control of every company in Germany whether that company liked it or not. They took control for national defense reasons. Anybody who said no got a lovely vacation in one of the lovely little camps. The U.S. airlines of the day were pressed into service in the Air Transport Command. So yes, Lufthansa, Diamler, Junkers, etc. did what they were told, which doesn't mean that the people in that company agreed with it. Much like the way Singer Sewing Machines built guns for the U.S. durning the war. It is more interesting to note that American Airlines used to code share with the Nazi Zeppelin, Hindenburg. That was in 1936 and 1937.