To best understand it we can use an historical comparison. In 1935 the Nazi government issued the Nuremberg Laws. This infamous legislation banned Jews from most professions, forbade marriage between Jews and non Jews, barred Jews from most social club and from many other setting where they could come into social contact with "true" Germans.
The Nazis, with their legislation, intended to isolate the Jews socially, professionally, culturally and economically. Only by eliminating Jewish interaction with non Jews could they proceed to the next step of their program, the physical isolation of Jews in concentration camps - and eventually, in 1942, they could not have implemented their "Final Solution" to the Jewish question. If Jews were not isolated, they would have had connections with the Aryan Germans and could have done something to oppose them. Isolation was a necessary prelude to exclusion and eventually extermination.
In more than one way, the attempts to isolate Israel and to eliminate Israel's name from maps and applications, is a XXI Century equivalent to the isolation promoted by the Nuremberg Laws. As the saying goes... "Out of sight, Out of Mind". In the Arab World, they even go a step further. Printed maps do not show Israel, replacing it for "Palestine" and Israeli cities are ignored...so Tel-Aviv does not exist, for example.
While protesting these exclusion sound as childish and the issue looks like a small one, the accumulation of these events does amount to solidifying the pretense that Israel doesn't exist and/or Israel doesn't have any right to Jerusalem. While it could be said that only "crazies" would fall for it, the reality is that even ten years ago this kind of delegitimization attacks were unthinkable and unheard off. Today they are accepted.
I'm pretty sure that in 1933, when Hitler came to power, many German Jews would have never thought that just two years later Germany would issue legislation making them non persons...
"Don't ask for whom the bells toll..."