What do some countries protest against Japan for?

Its usually pretty obvious when people are protesting exactly what they're protesting against. There's signs and chants and all sorts of things directly related to the issue at hand. With regard to japan, they're most likely to be protesting japans whaling industry, which still persists despite international bans on whaling, due to the endangered nature of many whale species.

During the war, Japan was pulled into the war just as the UnitedStates was pulled into WW1.

FDR, along with Britain - both of which were influenced by Zionism, forced Germany's compliance with the illegal terms of the Versailles Treaty that devastated Germany in 1919. After 14 years of oppression, Hitler aimed to restore Germany to its rightful place among the other European countries against the provisions set by the Allied countries.

After Britain declared war on Germany in 1939, FDR frothed at the mouth to get involved as well, but couldn't get Congressional support because the events in Europe had nothing to do with United States interest.

Roosevelt was determined to get into the war so he provoked Japan into attacking Pearl Harbor to force Congress's hand by bringing the war to America's back door.

Japan was blamed for starting that conflict just as Germany has always been blamed for starting the European conflict. They have been demonized unjustly - neither wanted war and to believe otherwise is a fool's errand. Neither country was large enough or powerful enough to even think about declaring war against countries that dwarfed them in size or military might.

The following quote explains exactly how it happened:

"People will provoke you until they bring out your ugly side, then play the victim when you go there." - unknown

Pushed hard enough and long enough and anyone will defend themselves.

Considering what they did until and during WW2, it's difficult for many including myself 

(had a cousin that was executed while a POW on the Bataan Death March) to forgive,

as even now they're among the more xenophobic / racist societies on the entire planet.

I give up - who is protesting against Japan (except for harvesting whales)?

It's the wrong shape. It's too long, and split into too many bits. Most countries think it should be shaped more like Australia, or Portugal, or some other place like that.