The only coup d'etat attempt on a U.S. president I'm aware of was against Franklin Roosevelt right after his first election. But this was actually foiled by a military man:

The Business Plot (also the Plot Against FDR and the White House Putsch) was according to an Congressional committee report a political conspiracy in 1933 wherein wealthy businessmen and corporations plotted a coup d’état to overthrow United States President Franklin D. Roosevelt. In 1934, the Business Plot was publicly revealed by retired Marine Corps Major General Smedley Butler testifying to the McCormack-Dickstein Congressional Committee. In his testimony, Butler claimed that a group of men had approached him as part of a plot to overthrow Roosevelt in a military coup. One of the alleged plotters, Gerald MacGuire, vehemently denied any such plot. In their final report, the Congressional committee supported Butler's allegations of the existence of the plot, but no prosecutions or further investigations followed, and the matter was mostly forgotten.
http://en.wikipedia.org/wiki/Business_plot


The novel "Seven Days In May" was a Cold War treatment of the idea, probably reflecting the tensions between the military and the Kennedy administration. I enjoyed the movie version, with Burt Lancaster as the hawkish ringleader and Kirk Douglas as his whistle-blower subordinate.
http://en.wikipedia.org/wiki/Seven_days_in_may