While Jewish interests were protected by Augustus and Julius Caesar, later emperors were not as accommodating of Jewish traditions and beliefs. Resistance of taxes levied by the Romans on the part of Jews in the occupied territories certainly contributed to the conflict. Conflict between the religious practices of the Jews and the Greeks intermingled in the area added to the tension.
A rapid succession of Roman emperors (due to political infighting in Rome) ranging from Nero to Vespasian (66-70 CE) culminated in the siege of Jerusalem and the destruction of the Temple.
Julius Caesar acted favorably towards the Jews and Jews were generally pretty well treated. Of course, there were wars between the Romans and the Jews in what is now Israel. However, those wars did not come about because of Roman suppression of Jewish practice. Instead, they were more about things like taxes.