Elder of Ziyon notes that the visa application website is run by a private firm, Computer Sciences Corporation, on behalf of the US State Department, and is the only officially authorized website for completing visa applications.
Curiously, while the website lists dozens of nations around the world, including rogue states like Iran, with their flags, there is no mention of Israel or the Israeli flag. Instead, two separate listings are made under the Middle East section: one for Jerusalem and one for Tel Aviv. Israel is, in fact, the only country whose reference is avoided and replaced with the names of cities.
Despite the separate links, both connect to the same page which services both the US Embassy in Tel Aviv and Consulate General in Jerusalem. Even here there is no mention or reference to the State of Israel and no image of the Israeli flag.
The failure to mention Israel even in connection to Tel Aviv has led to complaints to the State Department and US Embassy in Israel, but neither have responded to the complaints nor has the visa website yet been changed.
Source material can be found at this site.