Historical culture clashes between Japan and the U.S.
There are more differences between the United States and Japan than conflicting values during World War II. Cultural and societal differences between the two nations and its peoples shaped beliefs and perceptions and thus interactions within those societies and between them as well.
The Japanese media made sure to cast the United States in a negative light during the war. Even afterward, they would distort everything from Ted Kennedy's car accident and the death of Mary Jo Kopechne (claiming her death was murder) to important battles and events. Newspapers were the primary source of information/propaganda at that time, and during World War II, they tried to give the public what they wanted for morale.
Positive news was widely broadcast, but anything negative was also distorted or hidden. Sons or husbands who died during World War II were heroes, for sure, but the concept of suicide missions was unknown to the Japanese.
The dropping of "warning fliers" by the United States before the atomic bomb was let go is controversial. Some feel they were fair and that the Japanese denied their existence and failed to adequately warn the people. Others think they were a part of psychological warfare, really dropped after Anola Gay flew off to Hiroshima, and merely acting as a leery precursor of any future attacks.
The war and the role of the Japanese government caused uncertainty and hatred among the Japanese toward Americans. Any of the few white people living in Japan sometimes had their houses searched - not by the government, but by curious neighbors. "What I never got used to was my home being searched; nothing ever stolen, just investigated frequently," said one American woman living in Japan at the time (the only one for 60 miles).
She also received gift boxes of soaps, which she initially looked on nicely but later learned were insults, implying she was unclean. She was also spit on at times and cursed at as well.
And these sentiments lasted for a long time after the war.
The Japanese looked upon Americans as crude and immoral, by their standards, as a melting pot without a culture of its own. They also underestimated America's ability to unite for a cause and develop such a powerful bomb, perhaps because of the broadcasts by the Japanese media.
The United States citizens looked down upon the Japanese as well, disgusted by the brutality of medical experimentation on human subjects by the Japanese government (estimated to have killed between 3 to 10 million people). The treatment of POWs angered the United States as well; the notable photo of Australian Sgt. Leonard Siffleet about to be beheaded with a katana sword didn't help with anti-Japanese sentiments, which probably began with the "sneak attack" on Pearl Harbor.
Similarly to the actions of the Japanese media during World War II, the United States felt it necessary to dehumanize the enemy with bombs and even mutilization of Japanese war dead, of course along with interment camps. Their refusal to accept defeat angered and put off Americans, as did Japanese propaganda. Boycotts on Japanese products popped up in America.
Anger ensued after the discovery of bomb caches in Japanese hills and caves in the castle town of Kokura, the near target of the "Little Boy" bomb dropped on Hiroshima. The United States was to disarm and remove the bombs, then take them to the Sasebo Naval Station in Nagasaki. Japanese student groups acquired permits and organized riots against such action, even though peacekeepers would subdue them and their weapons and arms would be thrown right back at them.
Culture clashes and more continue to leave gaps between America and Japan. News of sexual slavery during WWII on the part of Japan, and anti-Japanese sentiments evident in American societal products and business, keep the nations apart.