I don't see the problem. American has a serious obesity problem, and many other countries are catching up. Much of this problem is caused by a horrible diet, including fast foods such as Mcdonalds. Subway is just capitalizing on it using their healthier image, artificial though that may be. They might be both scaring and amusing Germans with insulting Americans for being fat, but a very large percentage of Americans are fat, it isn't a good thing, and they're probably on average fatter than Germans.
I didn't think Super Size Me was a perticularly great movie, but it was in no way anti-American, unless crisizing the fast food industry is anti-American.