Shalom,
Indeed, one has to be careful facing rumors.
I have never heard of someone being turned back and who is Pakistani for no reasons and just because of his origin.
However, your rumor comes from the fact that in 2003 2 British of Pakistani origins commited a suicide terrorist (one of them succeded) attack at Mike's Place in Tel Aviv. Therefore the Israeli authorities or the airline you fly might be more careful and might ask you more questions but that's it. Unless you belong to a terrorist group there should be no problem.
Good luck!