I'm not 100% sure of why that date was chosen. It is very possibly related to a statement that Ayatollah Khamenei made in September 2015 declaring that Israel would not exist in 25 years, but that was reported on September 11. September 17, 2040 is Yom Kippur so perhaps the Iranians think that God will destroy the Jews after they do not repent properly on that date.
What do the Israelis have to repent for? Glad you asked. While much of the site is a rehash of the normal complaints about Israel we hear at the UN every day, the Iranians also have problems with Israel being way too liberal.
So for example there is a page about gay rights in Israel, where the website complains that "there is no doubt that Israel is the most tolerant of gays in the Middle East."
Likewise, Israel's tolerance for abortion - even abortion of little Zionist fetuses - is decried as another thing to hate about the Zionist entity.
Most of the rest of the site is just to gather everything bad about Israel they can find. It is always amusing how everyone can find Jews to be the representatives of everything they hate, no matter where they are politically.
(h/t Yoel)