|I am going to be really honest and state that I have not run into this prejudice. I wear makeup very rarely, and have never felt it to be in any way an issue.
I concur with the above.
I'm sorry OP, that you have run into this. I work in the legal profession and while I'm required to wear suits to court and to dress appropriately for the office, tons of my colleagues appear to be make-up free. I wear make-up simply because I have an uneven skin tone and the occassional break-out, but my guess is that no one even knows that I wear make-up.
I have worked in a variety of fields and have never encountered a "make-up policy." Oddly, I think that make-up was more heavily encouraged (socially) in the little rural town where I grew up in than in the major city where I currently reside. In fact, people were heavily made-up where I grew up - too heavily in my opinion. My own mother tried to get me to wear more make-up for years and then she finally gave up. I almost think it is a cultural thing (not in terms of ethniticity - but in terms of social status in some demographics).
Now, manicures and pedicures, that seems to be a real social requirement in my current town. In fact, I've gotten looks of distain from women on the subway and bus as they stare at my rather colorless and stubby nails. It seems that there are various levels of self-care that people find important. I find these attitudes more in the public sphere than in the workplace.