It sounds like he’s not really discriminating against you in the sense of treating your poorly, not giving your raises, etc. If that were the case I would simply try to find another job.
In the meantime the best you can do is be a kiddush Hashem. He thinks frum Jews are backwards. But if your attitude and behavior is better than his, then perhaps he will rethink his hostility, and he will be open to taking on more observance (and even perhaps realizing the error of his heterodox ways).
So do a great job, be super respectful to everyone, refrain from expressing any conservative political opinions (which will probably just make him hate you and stereotype frum Jews more), etc. Pray to Hashem in your own words that you can be a kiddush Hashem, and that he changes his attitudes. Hatzlacha!