It's the "deal" the Israeli government made with the Muslims after they captured Jerusalem in 1967, and with laws and policies since then. The Israeli government handed day-to-day control of the area to the Muslim Waqf religious authorities, overseen by the Jordanian government. Non-Muslims (including Jews of course) are not allowed to pray on the holy site for fear of offending Muslim worshippers.
Feed the alligator, and hope he doesn't eat you next.