As a matter of identification, I am Jewish.
To answer your question, the reason is often expressed as antisemitism.
I find that term "antisemite" imprecise. I like to understand what is going on in the mind of the "antisemite."
Might some be Palestinians whose families owned land in Palestine (not a country)? The families may have chosen to leave the land in 1948 planning to return after the war. Perhaps conditions of war in 1948 forced families to move.
There are other reasons.
I think the wording on a passport invokes allegiance.