Like the other girls said, if a stranger said so, probably not, if a loved one said so, yes.
Im not conceited either and dont have a lot of self esteem, but you do have to take into account jealousy. Some people would say that about you to make themselves feel better, or because they wish they could pull off your look or technique.
I know many times Ive seen really gorgeous girls or pictures of girls, and I want to think or say shes only pretty because of her gorgeous makeup, but most of the time, its not the case. Its natural beauty that is beautiful, makeup just enhances it, so a statement like "Shes only pretty with makeup on" is, IMO, shallow and usually untrue.