Pompey just decided to step in and have a peak, having helped the Pharisee high priest take power there as John Hyrcanus, against the Sadducees. I don't think he revealed much of what he saw and allowed them to purify it and seal it up again, leaving offerings. As I understood it the Romans stayed on relatively good terms at least as long as the time of Agrippa. It was unrest under Herod Agrippa II and the mismanagement of a Roman governor there that precipitated the catastrophe against Vespasian and Titus. Bar Kokhba came 60 years later, and by then they were certainly not popular. They were persecuted, like Christians, under the rule of Severus who was upholding the law. But the reasons as some have pointed out here, is the Romans didn't care for religions at odds with their own traditional beliefs, resisting the process of syncretism.