One factor the article doesn't mention is the strong possibility that the avalanche of legal and illegal immigrants from poor countries is dragging down our American average height. The article hints at this factor as follows:
Komlos and Lauderdale also found height inequality between American urbanites and residents of suburbs and rural areas. In Kansas, for example, white males are about as tall as their European peers; it's big cities like New York, where men are about 1.75 inches shorter than that, that drag America's average down.
This sounds like another good argument in favor of getting control of our borders and cutting off the illegal immigration of hordes of unskilled, dirt-poor laborers.