OK here are the reasons why Pakistani passport is not required for Israel.Whenever you hold a Pakistani passport here is a message on the passport.
The reason here is that Pakistan is a part of the Arab League on the boycott of Israel but still Pakistanis can visit Israel on other passports which have visa free access to Israel.Here is a map of all those nations which cancelled Israeli passport holders.
On the blue it is Israel
Light green is all those nation which reject Israeli passports but if you hold other passport you get the opportunity to visit Israel.
Dark green represents that any person holding Israeli stamps cannot visit those countries, even holding other passport.
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Actually the main reason is Belief or Faith on which both of these countries established.
Belief is separate land for Muslims to perform there religious activities without any distortion.
Belief is independent Jewish state after the world war II
So the main reason is that Pakistan has refused to recognize Israel.