Israeli ID cards are different from passports/citizenship. Palestinians are not allowed to fly out of Ben Gurion airport generally. The cards that Shin Bet is talking about can be used to obtain Lesse Passe and travel through one of the Jordanian border crossings. The measures employed by the IAA are against citizens of the state.
Neurologist and author Oliver Sacks dies at 82 (Haaretz)
from the article: Machsom Watch requests to monitor airport security checks