Ishida does not possess any deep hatred of Shinigami with the sole exception of Mayuri. He "I hate Shinigami" mantra was actually a projection of his self loathing for the time he hid while his grandfather was killed by hollows. He blamed the Shinigami for arriving late but more then that, he blamed his own in ability to save his grandfather. Notably, his grandfather, who was Ishida's mentor, did not hate Shinigami and wanted the remaining Quincy to work closely with them.