I wrote a piece on another blog about 3 years ago, that I think is still valid as a general rule with regard to wearing a Kippah at job interviews or at work. And I still believe that if an employer won't tolerate your wearing a Kippah you may not want to work there, but everyone needs to make his own decision. However, in your particular case, it sounds like your employer is violating Title VII of the Civil Rights Act of 1964, which ensures religious freedom (among other freedoms) in the workplace in the U.S. Of course, I don't know if you are located/working in the U.S., but if you are, it might be worth reporting it to the United States Equal Employment Opportunity Commission.

Just to paraphrase the closing paragraph from the other piece, what I have to say on the subject in general is this: it's a personal choice. If you feel wearing a Kippah is hurting you in your employment or job search, you have every right to take it off - and you have every right to put it back on at any point. However, be prepared to be made uncomfortable for doing so, and begin looking for a new job with an employer that can see past it - all while diligently doing your job. On the other hand, if you choose to wear it, I will give you the Berachah (blessing) given to me by a rabbi I consulted on the subject: You will get a job that is good for you (either by this one changing to become friendlier or another one), and being Moser Nefesh will come back to reward you, either in this world or the next. Even if it isn't about observance/Halachah, but you simply wear your Kippah as a badge of honor and Jewish pride, continue to do so because you will ultimately find something suitable, and your colleagues – particularly in an environment where they are willing to hire someone who is proud of his heritage and beliefs – will respect you for it.