I don't think it would have been feasible, by the shear numbers of German-heritage Americans at the time, to target them domestically or go after the motherland with firebombs and the atom bombs like Japan. By this point with the six million or so German immigrants over the previous 100 years "German-Americans" had to easily be the largest ethnic group in this country, although "Americanization" of most in the group was probably much greater than during WWI.
As done in many political cartoons from the time including those from Dr. Seuss, IMO it was much easier to portray and sell Japan and the Japanese as being "other" and repugnant or vile than the European axis alliance members, especially Germany, as there were very few Japanese and Asians in general in this country at the time. At the 1940 census roughly 90% of the country was white, and factoring in blacks accounted for close to 99.5% of the population.