If FDR’s response really was motivated by some overt prejudice against Jews, then that is what I would fault him for. But, I had not heard before that FDR had such a prejudice, and I wonder if the author is fair and accurate in his characterization of the private remarks which he uses to build his case. I am not ready to be convinced one way or another on this without more details.
No one has to be prejudiced to be against admitting large numbers of foreign refugees, potential genocide victims or not, whether they are Jews, South West African Hereros, Cambodians, Rwandan Tutsis, Iraqi Christians, Egyptian Copts or Burmese Rohingyans. Was FDR less prejudiced against Japanese Americans, the Chinese, the Gypsies, the Slavs and so on? Tens of millions of Chinese were killed by Imperial Japan without any suggestion that FDR should have imported millions of them in to keep them safe. Ditto with Gypsies and Slavs who were slaughtered like sheep by Nazi Germany.